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Lai J, Zhou Z, Hu K, Yu H, Su X, Niu X, Li H, Mao S. N6-methyladenosine methylation analysis of long noncoding RNAs and mRNAs in 5-FU-resistant colon cancer cells. Epigenetics 2024; 19:2298058. [PMID: 38145548 PMCID: PMC10761136 DOI: 10.1080/15592294.2023.2298058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023] Open
Abstract
N6 methyladenosine (m6A), methylation at the sixth N atom of adenosine, is the most common and abundant modification in mammalian mRNAs and non-coding RNAs. Increasing evidence shows that the alteration of m6A modification level could regulate tumour proliferation, metastasis, self-renewal, and immune infiltration by regulating the related expression of tumour genes. However, the role of m6A modification in colorectal cancer (CRC) drug resistance is unclear. Here, MeRIP-seq and RNA-seq techniques were utilized to obtain mRNA, lncRNA expression, and their methylation profiles in 5-Fluorouracil (5-FU)-resistant colon cancer HCT-15 cells and control cells. In addition, we performed detailed bioinformatics analysis as well as in vitro experiments of lncRNA to explore the function of lncRNA with differential m6A in CRC progression and drug resistance. In this study, we obtained the m6A methylomic landscape of CRC cells and resistance group cells by MeRIP-seq and RNA-seq. We identified 3698 differential m6A peaks, of which 2224 were hypermethylated, and 1474 were hypomethylated. Among the lncRNAs, 60 were hypermethylated, and 38 were hypomethylated. GO and KEGG analysis annotations showed significant enrichment of endocytosis and MAPK signalling pathways. Moreover, knockdown of lncRNA ADIRF-AS1 and AL139035.1 promoted CRC proliferation and invasive metastasis in vitro. lncRNA- mRNA network showed that ADIRF-AS1 and AL139035.1 May play a key role in regulating drug resistance formation. We provide the first m6A methylation profile in 5-FU resistance CRC cells and analyse the functions of differential m6A-modified mRNAs and lncRNAs. Our results indicated that differential m6A RNAs were significantly associated with MAPK signalling and endocytosis after induction of 5-FU resistance. Knockdown of LncRNA ADIRF-AS1 and AL139035.1 promotes CRC progression and might be critical in regulating drug resistance formation.
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Affiliation(s)
- Jie Lai
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - Zhiyong Zhou
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kan Hu
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - HongLong Yu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xingyao Su
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiaoqiang Niu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Huizi Li
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shengxun Mao
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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Yang H, Xie C, Wu YF, Cheng Y, Zhu DS, Guan YT. N 6-Methyladenosine (m 6A) Methylation Is Associated with the Immune Microenvironments in Acute Intracerebral Hemorrhage (ICH). Mol Neurobiol 2024; 61:1781-1793. [PMID: 37776495 DOI: 10.1007/s12035-023-03643-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/06/2023] [Indexed: 10/02/2023]
Abstract
Researchers have recently found that N6-methyladenosine (m6A) is a type of internal posttranscriptional modification that is essential in mammalian mRNA. However, the features of m6A RNA methylation in acute intracerebral hemorrhage (ICH) remain unknown. To explore differential methylations and to discover their functions in acute ICH patients, we recruited three acute ICH patients, three healthy controls, and an additional three patients and healthy controls for validation. The m6A methylation levels in blood samples from the two groups were determined by ultrahigh-performance liquid chromatography coupled with triple quadruple mass spectrometry (UPLC-QQQ-MS). Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was employed to identify differences in m6A modification, and the differentially expressed m6A-modified genes were confirmed by MeRIP-qPCR. We found no significant differences in the total m6A levels between the two groups but observed differential methylation peaks. Compared with the control group, the coding genes showing increased methylation following acute ICH were mostly involved in processes connected with osteoclast differentiation, the neurotrophin signaling pathway, and the spliceosome, whereas genes with reduced m6A modification levels after acute ICH were found to be involved in the B-cell and T-cell receptor signaling pathways. These results reveal that differentially m6A-modified genes may influence the immune microenvironments in acute ICH.
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Affiliation(s)
- Hong Yang
- Department of Neurology, The First Rehabilitation Hospital of Shanghai, School of Medicine, Tongji University, Shanghai, China
| | - Chong Xie
- Department of Neurology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi-Fan Wu
- Department of Neurology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuan Cheng
- Department of Neurology, The First Rehabilitation Hospital of Shanghai, School of Medicine, Tongji University, Shanghai, China
| | - De-Sheng Zhu
- Department of Neurology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yang-Tai Guan
- Department of Neurology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Department of Neurology, Shanghai Yangzhi Rehabilitation Hospital, School of Medicine, Tongji University, Shanghai, China.
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Xia W, Guo L, Su H, Li J, Lu J, Li H, Huang B. A low-cost, low-input method establishment for m6A MeRIP-seq. Biosci Rep 2024; 44:BSR20231430. [PMID: 38113135 PMCID: PMC10776898 DOI: 10.1042/bsr20231430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 12/03/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023] Open
Abstract
N6-methyladenosine (m6A) is a highly prevalent modification found in mammal mRNA molecules that plays a crucial role in the regulation of cellular function. m6A RNA immunoprecipitation sequencing (MeRIP-seq) has been frequently used in transcriptomics research to identify the location of m6A. MABE572 (Millipore) is the most widely utilized and efficient anti-m6A antibody for MeRIP-seq. However, due to the high dose and price of this antibody, which has also been taken off the market, we discovered that CST's anti-m6A antibody can be used instead of MABE572 to map the m6A transcriptome. In the present study, we performed different concentrations of the CST anti-m6A antibodies with the corresponding initiation RNA of HEK293T cells, 2.5 μg antibody with 1 μg total RNA, 1.25 μg antibody with 0.5 μg total RNA, and 1.25 μg antibody with 0.1 μg total RNA. By comparing the m6A peak calling, enriched motifs, alternative splicing events, and nuclear transcripts modified by m6A between the CST and Millipore libraries, it was found that the CST library presented similar data to Millipore, even at incredibly low doses. The volume and cost of antibodies are significantly reduced by this refined MeRIP-seq using CST antibody, making it convenient to map future large-scale sample m6A methylation.
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Affiliation(s)
- Wenjuan Xia
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Ling Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Huapeng Su
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Jincheng Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Jiafeng Lu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Hong Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Boxian Huang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
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Yao M, Cheng Z, Li X, Li Y, Ye W, Zhang H, Liu H, Zhang L, Lei Y, Zhang F, Lv X. N6-methyladenosine modification positively regulate Japanese encephalitis virus replication. Virol J 2024; 21:23. [PMID: 38243270 PMCID: PMC10799421 DOI: 10.1186/s12985-023-02275-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024] Open
Abstract
N6-methyladenosine (m6A) is present in diverse viral RNA and plays important regulatory roles in virus replication and host antiviral innate immunity. However, the role of m6A in regulating JEV replication has not been investigated. Here, we show that the JEV genome contains m6A modification upon infection of mouse neuroblast cells (neuro2a). JEV infection results in a decrease in the expression of m6A writer METTL3 in mouse brain tissue. METTL3 knockdown by siRNA leads to a substantial decrease in JEV replication and the production of progeny viruses at 48 hpi. Mechanically, JEV triggered a considerable increase in the innate immune response of METTL3 knockdown neuro2a cells compared to the control cells. Our study has revealed the distinctive m6A signatures of both the virus and host in neuro2a cells infected with JEV, illustrating the positive role of m6A modification in JEV infection. Our study further enhances understanding of the role of m6A modification in Flaviviridae viruses.
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Affiliation(s)
- Min Yao
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - Zhirong Cheng
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
- College of Life Science, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Xueyun Li
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
- College of Basic Medicine, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Yuexiang Li
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - Wei Ye
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - Hui Zhang
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - He Liu
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - Liang Zhang
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - Yingfeng Lei
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China
| | - Fanglin Zhang
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China.
| | - Xin Lv
- Department of Microbiology, Airforce Medical University, Xi'an, 710032, Shaanxi, China.
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Zheng X, Zhou B, Li Y, Zhong H, Huang Z, Gu M. Transcriptome-wide N 6-methyladenosine methylation profile of atherosclerosis in mice. BMC Genomics 2023; 24:774. [PMID: 38097926 PMCID: PMC10720251 DOI: 10.1186/s12864-023-09878-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Atherosclerosis (AS) is a critical pathological event during the progression of cardiovascular diseases. It exhibits fibrofatty lesions on the arterial wall and lacks effective treatment. N6-methyladenosine (m6A) is the most common modification of eukaryotic RNA and plays an important role in regulating the development and progression of cardiovascular diseases. However, the role of m6A modification in AS remains largely unknown. Therefore, in this study, we explored the transcriptome distribution of m6A modification in AS and its potential mechanism. METHODS Methylation Quantification Kit was used to detect the global m6A levels in the aorta of AS mice. Western blot was used to analyze the protein level of methyltransferases. Methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were used to obtain the first transcriptome range analysis of the m6A methylene map in the aorta of AS mice, followed by bioinformatics analysis. qRT-PCR and MeRIP-qRT-PCR were used to measure the mRNA and m6A levels in target genes. RESULTS The global m6A and protein levels of methyltransferase METTL3 were significantly increased in the aorta of AS mice. However, the protein level of demethylase ALKBH5 was significantly decreased. Through MeRIP-seq, we obtained m6A methylation maps in AS and control mice. In total, 26,918 m6A peaks associated with 13,744 genes were detected in AS group, whereas 26,157 m6A peaks associated with 13,283 genes were detected in the control group. Peaks mainly appeared in the coding sequence (CDS) regions close to the stop codon with the RRACH motif. Moreover, functional enrichment analysis demonstrated that m6A-containing genes were significantly enriched in AS-relevant pathways. Interestingly, a negative correlation between m6A methylation abundance and gene expression level was found through the integrated analysis of MeRIP-seq and RNA-seq data. Among the m6A-modified genes, a hypo-methylated but up-regulated (hypo-up) gene Fabp5 may be a potential biomarker of AS. CONCLUSIONS Our study provides transcriptome-wide m6A methylation for the first time to determine the association between m6A modification and AS progression. Our study lays a foundation for further exploring the pathogenesis of AS and provides a new direction for the treatment of AS.
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Affiliation(s)
- Xinbin Zheng
- Clinical Research Center, Hainan Provincial Hospital of Traditional Chinese Medicine, 570203, Haikou, Hainan, P. R. China
- Hainan Clinical Research Center for Preventive Treatment of Diseases, 570203, Haikou, Hainan, P. R. China
- Hospital of Chinese Medicine affiliated by Hainan Medical University, 570203, Haikou, Hainan, P. R. China
| | - Bo Zhou
- Department of Cardiology, Hainan Provincial Hospital of Traditional Chinese Medicine, 570203, Haikou, Hainan, P. R. China
- Hospital of Chinese Medicine affiliated by Hainan Medical University, 570203, Haikou, Hainan, P. R. China
| | - Yuzhen Li
- Clinical Research Center, Hainan Provincial Hospital of Traditional Chinese Medicine, 570203, Haikou, Hainan, P. R. China
- Hospital of Chinese Medicine affiliated by Hainan Medical University, 570203, Haikou, Hainan, P. R. China
| | - Hengren Zhong
- Clinical Research Center, Hainan Provincial Hospital of Traditional Chinese Medicine, 570203, Haikou, Hainan, P. R. China
- Hospital of Chinese Medicine affiliated by Hainan Medical University, 570203, Haikou, Hainan, P. R. China
| | - Zhengxin Huang
- Department of Cardiology, Hainan Provincial Hospital of Traditional Chinese Medicine, 570203, Haikou, Hainan, P. R. China.
- Hospital of Chinese Medicine affiliated by Hainan Medical University, 570203, Haikou, Hainan, P. R. China.
| | - Minhua Gu
- Department of Cardiology, Hainan Provincial Hospital of Traditional Chinese Medicine, 570203, Haikou, Hainan, P. R. China.
- Hospital of Chinese Medicine affiliated by Hainan Medical University, 570203, Haikou, Hainan, P. R. China.
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Zhao Y, Meng J, Song X, An Q. m 6A mRNA Methylation Analysis Provides Novel Insights into Pigmentation in Sheep Skin. Epigenetics 2023; 18:2230662. [PMID: 37389979 DOI: 10.1080/15592294.2023.2230662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/09/2023] [Accepted: 06/20/2023] [Indexed: 07/02/2023] Open
Abstract
N6-methyladenosine (m6A) is the most universal post-transcriptional modification of mRNA which may play important roles in verious species. However, the potential roles of m6A in the pigmentation of skin are not completely understood. To explore the role of m6A modification in pigmentation of sheep skin, we used MeRIP-seq and RNA-seq to profile the skin transcriptome in black and white coat color (n=3). Our results showed that an average of 7701 m6A peaks were obtained for all samples and the average length was 305.89 bp. The GGACUU sequence was the most enrichment motif and shared in black skin and white skin. The m6A peaks were mainly enriched in the CDS, 3'UTR and 5'UTR, especially in CDS region near the stop codon of the transcript. 235 significantly differential peaks were found in black skin vs. white skin. The KEGG signaling pathways of downregulated and upregulated m6A peaks were mainly enriched in AGE-RAGE signaling pathway in diabetic complications, Viral carcinogenesis, Transcriptional misregulation in cancer, ABC transporters, Basal transcription factors and Thyroid hormone synthesis (P value <0.05). For RNA-seq, 71 differently expressed genes (DEGs) were scanned in black skin vs. white skin. DEGs were significantly enriched in tyrosine metabolism, melanogenesis, neuroactive ligand-receptor interaction pathway (P value <0.05). Combined m6A-seq and RNA-seq analysis showed that the hyper-up genes and hypo-up genes were both enriched in ErbB signaling pathway (P value <0.05). In conclusion, it provide a basis for further research into the functions of m6A methylation modifications in pigmentation.
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Affiliation(s)
- Yuanyuan Zhao
- Guizhou Provincial Key Laboratory for Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren University, Tongren, Guizhou, P. R. China
| | - Jinzhu Meng
- Guizhou Provincial Key Laboratory for Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren University, Tongren, Guizhou, P. R. China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, P.R. China
| | - Xingchao Song
- Guizhou Provincial Key Laboratory for Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren University, Tongren, Guizhou, P. R. China
| | - Qingming An
- Guizhou Provincial Key Laboratory for Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren University, Tongren, Guizhou, P. R. China
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Krusnauskas R, Stakaitis R, Steponaitis G, Almstrup K, Vaitkiene P. Identification and comparison of m6A modifications in glioblastoma non-coding RNAs with MeRIP-seq and Nanopore dRNA-seq. Epigenetics 2023; 18:2163365. [PMID: 36597408 PMCID: PMC9980576 DOI: 10.1080/15592294.2022.2163365] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The most prominent RNA modification - N6-methyladenosine (m6A) - affects gene regulation and cancer progression. The extent and effect of m6A on long non-coding RNAs (lncRNAs) is, however, still not clear. The most established method for m6A detection is methylated RNA immunoprecipitation and sequencing (MeRIP-seq). However, Oxford Nanopore Technologies recently developed direct RNA-seq (dRNA-seq) method, allowing m6A identification at higher resolution and in its native form. We performed whole transcriptome sequencing of the glioblastoma cell line U87-MG with both MeRIP-seq and dRNA-seq. For MeRIP-seq, m6A peaks were identified using nf-core/chipseq, and for dRNA-seq - EpiNano pipeline. MeRIP-seq analysis revealed 5086 lncRNAs transcripts, while dRNA-seq identified 336 lncRNAs transcripts from which 556 and 198 were found to be m6A modified, respectively. While 24 lncRNAs with m6A overlapped between two methods. Gliovis database analysis revealed that the expression of the major part of identified overlapping lncRNAs was associated with glioma grade or patient survival prognosis. We found that the frequency of m6A occurrence in lncRNAs varied more than 9-fold throughout the provided list of 24 modified lncRNAs. The highest m6A frequency was detected in MIR1915HG, THAP9-AS1, MALAT1, NORAD1, and NEAT1 (49-88nt), while MIR99AHG, SNHG3, LOXL1-AS1, ILF3-DT showed the lowest m6A frequency (445-261nt). Taken together, (1) we provide a high accuracy list of 24 m6A modified lncRNAs of U87-MG cells; (2) we conclude that MeRIP-seq is more suitable for an initial m6A screening study, due to its higher lncRNA coverage, whereas dRNA-seq is most useful when more in-depth analysis of m6A quantity and precise location is of interest.Abbreviations: (dRNA-seq) direct RNA-seq, (GBM) glioblastoma, (LGG) low-grade glioma, (lncRNAs) long non-coding RNAs, (m6A) N6-methyladenosine, (MeRIP-seq) methylated RNA immunoprecipitation and sequencing, (ncRNA) non-coding RNA, (ONT) Oxford Nanopore Technologi; Lietuvos Mokslo Taryba.
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Affiliation(s)
- Raulas Krusnauskas
- Laboratory of Molecular Neurobiology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
| | - Rytis Stakaitis
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
| | - Giedrius Steponaitis
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
| | - Kristian Almstrup
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (Edmarc), Rigshospitalet, University of Copenhagen, GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Paulina Vaitkiene
- Laboratory of Molecular Neurobiology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
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Hua Y, Li X, Yin B, Huang J, Lu S, Wang C, Ke S, Xu Y, Qian B, Feng Z, Yu H, Ma Y. Comprehensive analysis of transcriptome-wide M 6A methylation for hepatic ischaemia reperfusion injury in mice. Epigenetics 2023; 18:2201716. [PMID: 37066716 PMCID: PMC10114981 DOI: 10.1080/15592294.2023.2201716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
N6-Methyladenosine (m6A) plays key roles in the regulation of biological functions and cellular mechanisms for ischaemia reperfusion (IR) injury in different organs. However, little is known about the underlying mechanisms of m6A-modified mRNAs in hepatic IR injury. In mouse models, liver samples were subjected to methylated RNA immunoprecipitation with high-throughput sequencing (MeRIP-seq) and RNA sequencing (RNA-seq). In total, 16917 m6A peaks associated with 4098 genes were detected in the sham group, whereas 21,557 m6A peaks associated with 5322 genes were detected in the IR group. There were 909 differentially expressed m6A peaks, 863 differentially methylated transcripts and 516 differentially m6A modification genes determined in both groups. The distribution of m6A peaks was especially enriched in the coding sequence and 3'UTR. Furthermore, we identified a relationship between differentially m6A methylated genes (fold change≥1.5/≤ 0.667, p value≤0.05) and differentially expressed genes (fold change≥1.5 and p value≤0.05) to obtain three overlapping predicted target genes (Fnip2, Phldb2, and Pcf11). Our study revealed a transcriptome-wide map of m6A mRNAs in hepatic IR injury and might provide a theoretical basis for future research in terms of molecular mechanisms.
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Affiliation(s)
- Yongliang Hua
- Department of Minimally Invasive Hepatic Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, Heilongjiang, China
- The First Department of General Surgery, the Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, China
| | - Xinglong Li
- Department of Minimally Invasive Hepatic Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, Heilongjiang, China
| | - Bing Yin
- Department of Minimally Invasive Hepatic Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, Heilongjiang, China
| | - Jingjing Huang
- Department of Minimally Invasive Hepatic Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, Heilongjiang, China
| | - Shounan Lu
- Department of Minimally Invasive Hepatic Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, Heilongjiang, China
| | - Chaoqun Wang
- Department of Minimally Invasive Hepatic Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, Heilongjiang, China
| | - Shanjia Ke
- Department of Minimally Invasive Hepatic Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, Heilongjiang, China
| | - Yanan Xu
- Department of Minimally Invasive Hepatic Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, Heilongjiang, China
| | - Baolin Qian
- Department of Minimally Invasive Hepatic Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, Heilongjiang, China
| | - Zhigang Feng
- Department of Minimally Invasive Hepatic Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, Heilongjiang, China
- Department of Pediatric Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Harbin, Heilongjiang, China
| | - Hongjun Yu
- Department of Minimally Invasive Hepatic Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, Heilongjiang, China
| | - Yong Ma
- Department of Minimally Invasive Hepatic Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, Heilongjiang, China
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Zhang J, Liu T, Wang Y, Yan X, Li Y, Xu F, Zhang R. Dynamic alterations of the transcriptome-wide m 6A methylome in cytogenetically normal acute myeloid leukaemia during initial diagnosis and relapse. Genomics 2023; 115:110725. [PMID: 37820824 DOI: 10.1016/j.ygeno.2023.110725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/08/2023] [Accepted: 10/08/2023] [Indexed: 10/13/2023]
Abstract
Accumulating studies have indicated that N6-methyladenosine (m6A) plays an important role in acute myeloid leukaemia (AML). However, little is known about the m6A methylome at a transcriptome-wide scale in AML patients. We obtained three pairs of bone marrow (BM) samples from cytogenetically normal AML patients at the timepoints of diagnosis (AML) and relapse (R_AML) and three BM samples from healthy donors used as normal controls (NCs). Methylated RNA immunoprecipitation next-generation sequencing (MeRIP-Seq) was conducted to identify differences in the m6A methylomes between AML and NC and between R_AML and AML. We identified a total of 11,076 and 11,962 differential m6A peaks in AML and R_AML group, respectively. These dysregulated m6A peaks were detected on all chromosomes, especially chr1, chr19 and chr17, and were mainly enriched in 3' untranslated regions, stop codon and coding sequence regions. Moreover, GO and KEGG analyses indicated that m6A -modified genes were significantly enriched in cancer-related biological functions and pathways. Additionally, we identified a link between the m6A methylome and RNA transcriptome via combined analyses of MeRIP-seq and RNA-seq data. In addition, 5 genes, HSPG2, HOMER3, TSPO2, CXCL12 and FUT1 regulated by m6A modification potentially, were shown to be related to the prognosis of AML patients. Additionally, we detected the mRNA expression of major m6A regulators and potential target mRNA on the leukemogenesis and found that the expression of IGF2BP2, HSPG2 and HOMER3 were upregulated in AML at the time of diagnosis. Moreover, their expression became downregulated after remission and then elevated again at relapse. Our study provides the first data on the differential m6A methylome in AML patients during initial diagnosis and relapse. This study demonstrates a novel relationship between m6A modification and AML relapse and paves the way for further studies aimed at elucidating the epigenic mechanisms involved in the relapse of AML.
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Affiliation(s)
- Jinjing Zhang
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Tong Liu
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yue Wang
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Xiaojing Yan
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yan Li
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Feng Xu
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Rui Zhang
- Department of Hematology, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China.
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10
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Peng Q, Qiao J, Li W, You Q, Hu S, Liu Y, Liu W, Hu K, Sun B. Global m6A methylation and gene expression patterns in human microglial HMC3 cells infected with HIV-1. Heliyon 2023; 9:e21307. [PMID: 38027859 PMCID: PMC10643106 DOI: 10.1016/j.heliyon.2023.e21307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
N6-methyladenosine (m6A) methylation of human immunodeficiency virus type 1 (HIV-1) RNA regulates viral replication, and the m6A of host RNA is affected by HIV-1 infection, but its global pattern and function are still unclear. In this study, we report that the number and position of m6A peaks in huge genes of human microglial HMC3 cells were modulated by a single cycle HIV-1 pseudotyped with VSV-G envelope glycoprotein infection using methylated RNA immunoprecipitation sequencing (MeRIP-seq). A conjoint analysis of MeRIP-seq and high-throughput sequencing for mRNA (RNA-seq) explored four groups of clearly classified genes, including 45 hyper-up (m6A-mRNA), 45 hyper-down, 120 hypo-up, and 54 hypo-down genes, in HIV-1 infected cells compared to uninfected ones. KEGG pathway analysis showed that these genes were mainly enriched in the Wnt and TNF signaling pathway, and cytokine-cytokine receptor interaction, which might be related to the immune response in HMC3 cells. And some of these genes might be associated with the pathway of axon guidance and neuroactive ligan-receptor interaction, which affect the neuronal state. However, the cognitive disorders caused by HIV-1 is associated with inflammatory changes that have not yet been well clarified. Furthermore, we confirmed the expression and m6A levels of four genes using RT-PCR and MeRIP-qPCR. Similar to the sequencing results, the expressions of these genes were significantly upregulated by HIV-1 infection. And the m6A level of IL-6 was downregulated, and those of HLA-B, CFB, and OLR1 were upregulated. These results suggest that HIV-1-induced changes in gene expression may be achieved through the regulation of methylation. Our study revealed the global m6A methylation and gene expression patterns under HIV-1 infection in human microglia, which might provide clues for understanding the interaction between HIV-1 and host cells and the cognitive disorders caused by HIV-1.
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Affiliation(s)
- Qian Peng
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and MolecularPharmaceutics, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education &Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), HubeiUniversity of Technology, Wuhan, China
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Jialu Qiao
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
- Department of Immunology, School of Medicine, Jianghan University, Wuhan, Hubei, 430056, China
| | - Weiling Li
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Qiang You
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Song Hu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Yuchen Liu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Wei Liu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Kanghong Hu
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and MolecularPharmaceutics, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education &Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), HubeiUniversity of Technology, Wuhan, China
| | - Binlian Sun
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
- Department of Immunology, School of Medicine, Jianghan University, Wuhan, Hubei, 430056, China
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11
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Zhang T, Yu B, Cai Z, Jiang Q, Fu X, Zhao W, Wang H, Gu Y, Zhang J. Regulatory role of N 6-methyladenosine in intramuscular fat deposition in chicken. Poult Sci 2023; 102:102972. [PMID: 37573849 PMCID: PMC10448335 DOI: 10.1016/j.psj.2023.102972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/15/2023] Open
Abstract
Intramuscular fat (IMF) has a pivotal influence on meat quality, with its deposition being a multifaceted physiological interaction of several regulatory factors. N6-methyladenosine (m6A), the preeminent epigenetic alteration among eukaryotic RNA modifications, holds a crucial role in moderating post-transcriptional gene expression. However, there is a dearth of comprehensive understanding regarding the functional machinery of m6A modification in the context of IMF deposition in poultry. Our current study entails an analysis of the disparities in IMF within the breast and leg of 180-day-old Jingyuan chickens. We implemented methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to delve into the distribution of m6A and its putative regulatory frameworks on IMF deposition in chickens. The findings demonstrated a markedly higher IMF content in leg relative to breast (P < 0.01). Furthermore, the expression of METTL14, WTAP, FTO, and ALKBH5 was significantly diminished in comparison to that of breast (P < 0.01). The m6A peaks in the breast and leg primarily populated 3'untranslated regions (3'UTR) and coding sequence (CDS) regions. The leg, when juxtaposed with the breast, manifested 176 differentially methylated genes (DMGs), including 151 hyper-methylated DMGs and 25 hypo-methylated DMGs. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed a pronounced enrichment of DMGs in the biosynthesis of amino acids, peroxisome, Fatty acid biosynthesis, fatty acid elongation, and cell adhesion molecules (CAMs) pathways. Key DMGs, namely ECH1, BCAT1, and CYP1B1 were implicated in the regulation of muscle lipid anabolism. Our study offers substantial insight and forms a robust foundation for further exploration of the functional mechanisms of m6A modification in modulating IMF deposition. This holds profound theoretical importance for improving and leveraging meat quality in indigenous chicken breeds.
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Affiliation(s)
- Tong Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Baojun Yu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Zhengyun Cai
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Qiufei Jiang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Xi Fu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Wei Zhao
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Haorui Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yaling Gu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Juan Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China.
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Yu Y, Lu S, Liu X, Li Y, Xu J. Identification and analysis of RNA-5-methylcytosine-related key genes in osteoarthritis. BMC Genomics 2023; 24:539. [PMID: 37700248 PMCID: PMC10496305 DOI: 10.1186/s12864-023-09651-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND 5-methylcytosine (m5C) modification is widely associated with many biological and pathological processes. However, knowledge of m5C modification in osteoarthritis (OA) remains lacking. Thus, our study aimed to identify common m5C features in OA. RESULTS In the present study, we identified 1395 differentially methylated genes (DMGs) and 1673 differentially expressed genes (DEGs) using methylated RNA immunoprecipitation next-generation sequencing (MeRIP-seq) and RNA-sequencing. A co-expression analysis of DMGs and DEGs showed that the expression of 133 genes was significantly affected by m5C methylation. A protein-protein interaction network of the 133 genes was constructed using the STRING database, and the cytoHubba plug-in of Cytoscape was used to hub genes were screen out 11 hub genes, including MMP14, VTN, COL15A1, COL6A2, SPARC, COL5A1, COL6A3, COL6A1, COL8A2, ADAMTS2 and COL7A1. The Pathway enrichment analysis by the ClueGO and CluePedia plugins in Cytoscape showed that the hub genes were significantly enriched in collagen degradation and extracellular matrix degradation. CONCLUSIONS Our study indicated that m5C modification might play an important role in OA pathogenesis, and the present study provides worthwhile insight into identifying m5C-related therapeutic targets in OA.
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Affiliation(s)
- Yang Yu
- Department of Orthopedics, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shitao Lu
- Department of Orthopedics, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoming Liu
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Yu Li
- Department of Orthopedics, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianzhong Xu
- Department of Orthopedics, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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13
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Zou K, Dong H, Li M, Zhang Y, Zhang K, Song D, Chu C. Comprehensive analysis of transcriptome-wide N6-methyladenosine methylomes in the Barrett's esophagus in rats. Genomics 2023; 115:110687. [PMID: 37454940 DOI: 10.1016/j.ygeno.2023.110687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/22/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
PURPOSE As the most abundant RNA modification, N6-methyladenosine (m6A) methylation plays crucial roles in various diseases. The aim of this study is to comprehensively map the landscape of the mRNA m6A modification pattern in Barrett's esophagus (BE) in order to find key genes and potential therapy for BE and even esophageal adenocarcinoma (EAC). METHODS Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA-sequencing (RNA-seq) were performed to compare the difference in mRNA m6A methylation and differentially expressed mRNAs between BE and normal control (NC) tissues. Bioinformatics analysis was used to describe the m6A modification pattern and specific genes in BE and NC tissues. RESULTS Through MeRIP-seq, we obtained m6A methylation profiling in BE and NC tissues. In total, 11,026 unique peaks were detected in the BE groups, whereas 8564 unique peaks were detected in the NC groups. Peaks were primarily enriched within CDS with GGACU motifs and most of the peaks were within 1000 bp in width. Moreover, functional enrichment analysis demonstrated that hypermethylated and hypomethylated genes were significantly enriched in coronavirus disease pathway, calcium signaling pathway and MAPK signaling pathways. Furthermore, PPI network was conducted and 18 hub genes were identified via STRING database and Cystoscope. Among them, ACTA1, CDC20, CKM, KIF20a, MYH11, TPM2, MYL9, DES, TNNT3 were overexpressed in EAC in the GEPIA gene bank and TPM1, KIF20a impaired patients' survival in the Kaplan-Meier plotter database. Finally, functional enrichment analysis demonstrated that co-expressed genes of TPM1 were significantly enriched in calcium signaling pathway, cGMP-PKG signaling pathway and PI3K-Akt signaling pathway. CONCLUSION Our study is the first to perform comprehensive and transcriptome-wide maps to identify the potential roles played by m6A methylation in BE, which widely involved in oxidative stress. This foresees a guiding role in revealing the molecular mechanism of m6A-mediated genes that govern the pathogenesis and progression of BE and EAC.
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Affiliation(s)
- Ke Zou
- Central Hospital Affiliated to Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250013, China; Jinan Central Hospital, Shandong University, No. 105, Jiefang Road, Jinan, Shandong 250013, China; Jinan Digestive Diseases Clinical Research Center, No. 105, Jiefang Road, Jinan, Shandong 250013, China; Jinan Key Translational Research Laboratory in Gastroenterology, No. 105, Jiefang Road, Jinan, Shandong 250013, China; Shandong University, No. 44, Wenhua west Road, Jinan, Shandong 250102, China
| | - Hui Dong
- Central Hospital Affiliated to Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250013, China; Jinan Central Hospital, Shandong University, No. 105, Jiefang Road, Jinan, Shandong 250013, China; Shandong University, No. 44, Wenhua west Road, Jinan, Shandong 250102, China
| | - Mengmeng Li
- Central Hospital Affiliated to Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250013, China; Jinan Central Hospital, Shandong University, No. 105, Jiefang Road, Jinan, Shandong 250013, China; Shandong University, No. 44, Wenhua west Road, Jinan, Shandong 250102, China
| | - Ying Zhang
- Central Hospital Affiliated to Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250013, China
| | - Kai Zhang
- Department of Internal Medicine, Weifang Medical University, Weifang, China
| | - Danlin Song
- Department of Internal Medicine, Weifang Medical University, Weifang, China
| | - Chuanlian Chu
- Central Hospital Affiliated to Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250013, China; Jinan Central Hospital, Shandong University, No. 105, Jiefang Road, Jinan, Shandong 250013, China; Jinan Digestive Diseases Clinical Research Center, No. 105, Jiefang Road, Jinan, Shandong 250013, China; Jinan Key Translational Research Laboratory in Gastroenterology, No. 105, Jiefang Road, Jinan, Shandong 250013, China; Shandong University, No. 44, Wenhua west Road, Jinan, Shandong 250102, China.
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14
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Zhao X, Li X, Li L, Zhang Y, Wu F, Yin R, Yuan M, Li X. Alterations of the m 6A Methylation Induced by TGF-β2 in ARPE-19 Cells. FRONT BIOSCI-LANDMRK 2023; 28:148. [PMID: 37525909 DOI: 10.31083/j.fbl2807148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/16/2023] [Accepted: 03/02/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND N6-methyladenosine (m6A) participates in diverse physiological processes and contributes to many pathological conditions. Epithelial-mesenchymal transition (EMT) of retinal pigmental epithelial (RPE) cells plays an essential role in retinal-related diseases, and transforming growth factor β2 (TGF-β2) is known to induce EMT in vitro. However, the effect of TGF-β2 on m6A methylation in RPE cells is not yet known. METHODS RNA-seq and MeRIP-seq were performed to analyze changes at the mRNA and m6A levels after TGF-β2 treatment of human ARPE-19 cells. mRNA levels and total m6A levels were subsequently validated. RESULTS Sequencing revealed 929 differentially expressed genes and 7328 differentially methylated genes after TGF-β2 treatment. Conjoint analysis identified 290 genes related to microtubule cytoskeleton, focal adhesion, ECM-receptor interaction, cell division, cell cycle, AGE-RAGE, PI3K-Akt and cGMP-PKG pathways. Further analysis revealed that 12 EMT-related genes were altered at the mRNA and m6A levels after TGF-β2 treatment (CALD1, CDH2, FN1, MMP2, SPARC, KRT7, CLDN3, ELF3, FGF1, LOXL2, SHROOM3 and TGFBI). Moreover, the total m6A level was also reduced. CONCLUSIONS This study revealed the transcriptional profiling of m6A modification induced by TGF-β2 in RPE cells. Novel connections were discovered between m6A modification and TGF-β2-induced EMT, suggesting that m6A may play crucial roles in the EMT process.
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Affiliation(s)
- Xueru Zhao
- Department of Ophthalmology, Henan Provincial People's Hospital, 450003 Zhengzhou, Henan, China
- Henan Key Laboratory of Ophthalmology and Visual Science, Henan Eye Hospital, Henan Eye Institute, 450003 Zhengzhou, Henan, China
- Department of Ophthalmology, People's Hospital of Zhengzhou University, 450003 Zhengzhou, Henan, China
- Department of Ophthalmology, People's Hospital of Henan University, 450003 Zhengzhou, Henan, China
| | - Xue Li
- Department of Ophthalmology, Henan Provincial People's Hospital, 450003 Zhengzhou, Henan, China
- Henan Key Laboratory of Ophthalmology and Visual Science, Henan Eye Hospital, Henan Eye Institute, 450003 Zhengzhou, Henan, China
- Department of Ophthalmology, People's Hospital of Zhengzhou University, 450003 Zhengzhou, Henan, China
- Department of Ophthalmology, People's Hospital of Henan University, 450003 Zhengzhou, Henan, China
| | - Lingke Li
- Department of Ophthalmology, Henan Provincial People's Hospital, 450003 Zhengzhou, Henan, China
- Department of Ophthalmology, People's Hospital of Henan University, 450003 Zhengzhou, Henan, China
| | - Yongya Zhang
- Department of Ophthalmology, Henan Provincial People's Hospital, 450003 Zhengzhou, Henan, China
- Department of Ophthalmology, People's Hospital of Zhengzhou University, 450003 Zhengzhou, Henan, China
| | - Fei Wu
- Department of Ophthalmology, Henan Provincial People's Hospital, 450003 Zhengzhou, Henan, China
- Department of Ophthalmology, People's Hospital of Zhengzhou University, 450003 Zhengzhou, Henan, China
| | - Ruijie Yin
- Department of Ophthalmology, Henan Provincial People's Hospital, 450003 Zhengzhou, Henan, China
- Henan Key Laboratory of Ophthalmology and Visual Science, Henan Eye Hospital, Henan Eye Institute, 450003 Zhengzhou, Henan, China
- Department of Ophthalmology, People's Hospital of Zhengzhou University, 450003 Zhengzhou, Henan, China
- Department of Ophthalmology, People's Hospital of Henan University, 450003 Zhengzhou, Henan, China
| | - Min Yuan
- Department of Ophthalmology, Henan Provincial People's Hospital, 450003 Zhengzhou, Henan, China
- Henan Key Laboratory of Ophthalmology and Visual Science, Henan Eye Hospital, Henan Eye Institute, 450003 Zhengzhou, Henan, China
- Department of Ophthalmology, People's Hospital of Zhengzhou University, 450003 Zhengzhou, Henan, China
- Department of Ophthalmology, People's Hospital of Henan University, 450003 Zhengzhou, Henan, China
| | - Xiaohua Li
- Department of Ophthalmology, Henan Provincial People's Hospital, 450003 Zhengzhou, Henan, China
- Henan Key Laboratory of Ophthalmology and Visual Science, Henan Eye Hospital, Henan Eye Institute, 450003 Zhengzhou, Henan, China
- Department of Ophthalmology, People's Hospital of Zhengzhou University, 450003 Zhengzhou, Henan, China
- Department of Ophthalmology, People's Hospital of Henan University, 450003 Zhengzhou, Henan, China
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Miyake K, Costa Cruz PH, Nagatomo I, Kato Y, Motooka D, Satoh S, Adachi Y, Takeda Y, Kawahara Y, Kumanogoh A. A cancer-associated METTL14 mutation induces aberrant m6A modification, affecting tumor growth. Cell Rep 2023; 42:112688. [PMID: 37355987 DOI: 10.1016/j.celrep.2023.112688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/25/2023] [Accepted: 06/08/2023] [Indexed: 06/27/2023] Open
Abstract
The methyltransferase-like 3 (METTL3)-/METTL14-containing complex predominantly catalyzes N6-methyladenosine (m6A) modification, which affects mRNA stability. Although the METTL14 R298P mutation is found in multiple cancer types, its biological effects are not completely understood. Here, we show that the heterozygous R298P mutation promotes cancer cell proliferation, whereas the homozygous mutation reduces proliferation. Methylated RNA immunoprecipitation sequencing analysis indicates that the R298P mutation reduces m6A modification at canonical motifs. Furthermore, this mutation induces m6A modification at aberrant motifs, which is evident only in cell lines harboring the homozygous mutation. The aberrant recognition of m6A modification sites alters the methylation efficiency at surrounding canonical motifs. One example is c-MET mRNA, which is highly methylated at canonical motifs close to the aberrantly methylated sites. Consequently, c-MET mRNA is severely destabilized, reducing c-Myc expression and suppressing cell proliferation. These data suggest that the METTL14 R298P mutation affects target recognition for m6A modification, perturbing gene expression patterns and cell growth.
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Affiliation(s)
- Kotaro Miyake
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Pedro Henrique Costa Cruz
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Izumi Nagatomo
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuki Kato
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shingo Satoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuichi Adachi
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; Department of Immunopathology, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan.
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16
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Meng H, Li Z, Wang L, Lyu L, Liu S, Wei R, Ni B, Liu F. Cells at early and late stages of infection with Senecavirus A: Comparative analysis of N 6-methyladenosine modification on mRNAs. Virology 2023; 585:186-195. [PMID: 37379620 DOI: 10.1016/j.virol.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Infection with Senecavirus A (SVA) causes differential phenotypes in cells. In this study, cells were inoculated with SVA for culture. At 12 and 72 h post infection, cells were independently harvested for high-throughput RNA sequencing, and further methylated RNA immunoprecipitation sequencing. The resultant data were comprehensively analyzed for mapping N6-methyladenosine (m6A)-modified profiles of SVA-infected cells. More importantly, m6A-modified regions were identified in the SVA genome. A dataset of m6A-modified mRNAs was generated for screening out differentially m6A-modified mRNAs, further subjected to a series of in-depth analyses. This study not only showed statistical differentiation of m6A-modified sites between two SVA-infected groups, but also demonstrated that SVA genome, as a positive-sense, single-stranded mRNA, itself could be modified through the m6A pattern. Out of the six samples of SVA mRNAs, only three were identified to be m6A-modified, implying that the epigenetic effect might not be a crucial driving force for SVA evolution.
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Affiliation(s)
- Hailan Meng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ziwei Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China; Surveillance Laboratory of Livestock Diseases, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao, 266109, China
| | - Liangpeng Lyu
- Qingdao Workstation of Animal Husbandry, Qingdao, 266199, China
| | - Shuqing Liu
- Qingdao Center for Animal Disease Control & Prevention, Qingdao, 266199, China
| | - Rong Wei
- Surveillance Laboratory of Livestock Diseases, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Bo Ni
- Surveillance Laboratory of Livestock Diseases, China Animal Health and Epidemiology Center, Qingdao, 266032, China.
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
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Li H, Lin J, Cheng S, Chi J, Luo J, Tang Y, Zhao W, Shu Y, Liu X, Xu C. Comprehensive analysis of differences in N6-methyladenosine RNA methylomes in Helicobacter pylori infection. Front Cell Dev Biol 2023; 11:1136096. [PMID: 37363723 PMCID: PMC10289286 DOI: 10.3389/fcell.2023.1136096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/13/2023] [Indexed: 06/28/2023] Open
Abstract
Background: Helicobacter pylori (H.pylori) infection is an important factor in the occurrence of human gastric diseases, but its pathogenic mechanism is not clear. N6-methyladenosine (m6A) is the most prevalent reversible methylation modification in mammalian RNA and it plays a crucial role in controlling many biological processes. However, there are no studies reported that whether H. pylori infection impacts the m6A methylation of stomach. In this study, we measured the overall level changes of m6A methylation of RNA under H. pylori infection through in vitro and in vivo experiment. Methods: The total quantity of m6A was quantified in gastric tissues of clinical patients and C57 mice with H. pylori infection, as well as acute infection model [H. pylori and GES-1 cells were cocultured for 48 h at a multiplicity of infection (MOI) from of 10:1 to 50:1]. Furthermore, we performed m6A methylation sequencing and RNA-sequencing on the cell model and RNA-sequencing on animal model. Results: Quantitative detection of RNA methylation showed that H. pylori infection group had higher m6A modification level. M6A methylation sequencing identified 2,107 significantly changed m6A methylation peaks, including 1,565 upregulated peaks and 542 downregulated peaks. A total of 2,487 mRNA was upregulated and 1,029 mRNA was downregulated. According to the comprehensive analysis of MeRIP-seq and RNA-seq, we identified 200 hypermethylation and upregulation, 129 hypermethylation but downregulation, 19 hypomethylation and downregulation and 106 hypomethylation but upregulation genes. The GO and KEGG pathway analysis of these differential methylation and regulatory genes revealed a wide range of biological functions. Moreover, combining with mice RNA-seq results, qRT- PCR showed that m6A regulators, METTL3, WTAP, FTO and ALKBH5, has significant difference; Two key genes, PTPN14 and ADAMTS1, had significant difference by qRT- PCR. Conclusion: These findings provide a basis for further investigation of the role of m6A methylation modification in H. pylori-associated gastritis.
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Affiliation(s)
- Huan Li
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jiahui Lin
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Sha Cheng
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jingshu Chi
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ju Luo
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yu Tang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Wenfang Zhao
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yufeng Shu
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xiaoming Liu
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Canxia Xu
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
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Yu B, Liu J, Cai Z, Wang H, Feng X, Zhang T, Ma R, Gu Y, Zhang J. RNA N 6-methyladenosine profiling reveals differentially methylated genes associated with intramuscular fat metabolism during breast muscle development in chicken. Poult Sci 2023; 102:102793. [PMID: 37276703 PMCID: PMC10258505 DOI: 10.1016/j.psj.2023.102793] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 06/07/2023] Open
Abstract
Intramuscular fat (IMF) is an important indicator for determining meat quality, and IMF deposition during muscle development is regulated by a complex molecular network involving multiple genes. The N6-methyladenosine (m6A) modification of mRNA plays an important regulatory role in muscle adipogenesis. However, the distribution of m6A and its role in IMF metabolism in poultry has not been reported. In the present study, a transcriptome-wide m6A profile was constructed using methylated RNA immunoprecipitation sequence (MeRIP-seq) and RNA sequence (RNA-seq) to explore the potential mechanism of regulating IMF deposition in the breast muscle based on the comparative analysis of IMF differences in the breast muscles of 42 (group G), 126 (group S), and 180-days old (group M) Jingyuan chickens. The findings revealed that the IMF content in the breast muscle increased significantly with the increase in the growth days of the Jingyuan chickens (P < 0.05). The m6A peak in the breast muscles of the 3 groups was highly enriched in the coding sequence (CDS) and 3' untranslated regions (3' UTR), which corresponded to the consensus motif RRACH. Moreover, we identified 129, 103, and 162 differentially methylated genes (DMGs) in the breast muscle samples of the G, S, and M groups, respectively. Functional enrichment analyses revealed that DMGs are involved in many physiological activities of muscle fat anabolism. The m6A-induced ferroptosis pathway was identified in breast muscle tissue as a new target for regulating IMF metabolism. In addition, association analysis demonstrated that LMOD2 and its multiple m6A negatively regulated DMGs are potential regulators of IMF differential deposition in muscle. The findings of the present study provide a solid foundation for further investigation into the potential role of m6A modification in regulating chicken fat metabolism.
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Affiliation(s)
- Baojun Yu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Jiamin Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Zhengyun Cai
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Haorui Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Xiaofang Feng
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Tong Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Ruoshuang Ma
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yaling Gu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Juan Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China.
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Li S, Zhou H, Liang Y, Yang Q, Zhang J, Shen W, Lei L. Integrated analysis of transcriptome-wide m 6A methylation in a Cd-induced kidney injury rat model. Ecotoxicol Environ Saf 2023; 256:114903. [PMID: 37054473 DOI: 10.1016/j.ecoenv.2023.114903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/28/2022] [Accepted: 04/09/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Accumulating evidence has demonstrated that N6-methyladenosine (m6A) plays important roles in a variety of diseases. However, the specific functions of m6A in CdCl2-induced kidney injury remain unclear. OBJECTIVE Here, we investigate a transcriptome-wide map of m6A modifications and explore the effects of m6A on Cd-induced kidney injury. MATERIALS AND METHODS The rat kidney injury model was constructed by subcutaneous injection of CdCl2 (0.5, 1.0, and 2.0 mg/kg). The m6A levels were measured by colorimetry. The level of expression of m6A-related enzymes were detected by reverse transcription quantitative real-time PCR analysis. Transcriptome-wide m6A methylome in CdCl2 (2.0 mg/kg) and the control group were profiled by methylated RNA immunoprecipitation sequencing (MeRIP-seq). Subsequently, the sequencing data were analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), while gene set enrichment analysis (GSEA) confirmed the functional enrichment pathways of sequencing genes. In addition, a protein-protein interaction (PPI) network was applied to select hub genes. RESULTS The levels of m6A and m6A regulators (METTL3, METTL14, WTAP, YTHDF2) were significantly increased in CdCl2 groups. We identified a total of 2615 differentially expressed m6A peaks, 868 differentially expressed genes and 200 genes with significant changes in both m6A modification and gene expression levels. GO, KEGG, and GSEA analyses indicated that these genes were mainly enriched in inflammation and metabolism-related pathways such as in IL-17 signaling and fatty acid metabolism. According the result of the conjoint analysis, we identified the top ten hub genes (Fos, Hsp90aa1, Gata3, Fcer1g, Cftr, Cspg4, Atf3, Cdkn1a, Ptgs2, and Npy) which may be regulated by m6A and involve in CdCl2-induced kidney damage. CONCLUSION This study established a m6A transcriptional map in a CdCl2-induced kidney injury model and suggested that m6A may affect CdCl2 induced kidney injury via regulated the inflammation and metabolism related gene.
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Affiliation(s)
- Shuangjing Li
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Han Zhou
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Yufen Liang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Qian Yang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Jiachen Zhang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Weitong Shen
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Lijian Lei
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China.
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20
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Wu K, Chang F, Li W, Wei D, Cao S, Xie Y, Li C, Lei D. Preliminary study based on methylation and transcriptome gene sequencing of lncRNAs and immune infiltration in hypopharyngeal carcinoma. Front Oncol 2023; 13:1117622. [PMID: 37182154 PMCID: PMC10168126 DOI: 10.3389/fonc.2023.1117622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/21/2023] [Indexed: 05/16/2023] Open
Abstract
Background Hypopharyngeal squamous cell cancer (HSCC) is one of the most malignant tumors of the head and neck. It is not easy to detect in the early stage due to its hidden location; thus, lymph node metastasis is highly likely at diagnosis, leading to a poor prognosis. It is believed that epigenetic modification is related to cancer invasion and metastasis. However, the role of m6A-related lncRNA in the tumor microenvironment (TME) of HSCC remains unclear. Methods The whole transcriptome and methylation sequencing of 5 pairs of HSCC tissues and adjacent tissues were performed to identify the methylation and transcriptome profiles of lncRNAs. The biological significance of lncRNAs differentially expressing the m6A peak was analyzed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. By constructing an m6A lncRNA-microRNA network, the mechanism of m6A lncRNAs in HSCC was analyzed. The relative expression levels of selected lncRNAs were examined by quantitative polymerase chain reaction. The CIBERSORT algorithm was used to evaluate the relative proportion of immune cell infiltration in HSCC and paracancerous tissues. Results Based on an in-depth analysis of the sequencing results, 14413 differentially expressed lncRNAs were revealed, including 7329 up-regulated and 7084 down-regulated lncRNAs. Additionally, 4542 up-methylated and 2253 down-methylated lncRNAs were detected. We demonstrated methylation patterns and gene expression profiles of lncRNAs of HSCC transcriptome. In the intersection analysis of lncRNAs and methylated lncRNAs, 51 lncRNAs with up-regulated transcriptome and methylation and 40 lncRNAs with down-regulated transcriptome and methylation were screened, and significantly differentiated lncRNAs were further studied. In the immune cell infiltration analysis, B cell memory was significantly elevated in cancer tissue, while γδT cell amount was significantly decreased. Conclusion m6A modification of lncRNAs might be involved in HSCC pathogenesis. Infiltration of immune cells in HSCC might provide a new direction for its treatment. This study provides new insights for exploring the possible HSCC pathogenesis and searching for new potential therapeutic targets.
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Affiliation(s)
- Kainan Wu
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, NHC Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, Shandong, China
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Fen Chang
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, NHC Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, Shandong, China
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Wenming Li
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, NHC Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, Shandong, China
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Dongmin Wei
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, NHC Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, Shandong, China
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shengda Cao
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, NHC Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, Shandong, China
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yulin Xie
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, NHC Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, Shandong, China
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Ce Li
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, NHC Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, Shandong, China
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Dapeng Lei
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, NHC Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, Shandong, China
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
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Duan D, Tang W, Wang R, Guo Z, Feng H. Evaluation of epitranscriptome-wide N6-methyladenosine differential analysis methods. Brief Bioinform 2023; 24:7111718. [PMID: 37039682 DOI: 10.1093/bib/bbad139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 04/12/2023] Open
Abstract
RNA methylation has emerged recently as an active research domain to study post-transcriptional alteration in gene expression regulation. Various types of RNA methylation, including N6-methyladenosine (m6A), are involved in human disease development. As a newly developed sequencing biotechnology to quantify the m6A level on a transcriptome-wide scale, MeRIP-seq expands RNA epigenetics study in both basic and clinical applications, with an upward trend. One of the fundamental questions in RNA methylation data analysis is to identify the Differentially Methylated Regions (DMRs), by contrasting cases and controls. Multiple statistical approaches have been recently developed for DMR detection, but there is a lack of a comprehensive evaluation for these analytical methods. Here, we thoroughly assess all eight existing methods for DMR calling, using both synthetic and real data. Our simulation adopts a Gamma-Poisson model and logit linear framework, and accommodates various sample sizes and DMR proportions for benchmarking. For all methods, low sensitivities are observed among regions with low input levels, but they can be drastically boosted by an increase in sample size. TRESS and exomePeak2 perform the best using metrics of detection precision, FDR, type I error control and runtime, though hampered by low sensitivity. DRME and exomePeak obtain high sensitivities, at the expense of inflated FDR and type I error. Analyses on three real datasets suggest differential preference on identified DMR length and uniquely discovered regions, between these methods.
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Affiliation(s)
- Daoyu Duan
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA
| | - Wen Tang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA
| | - Runshu Wang
- Department of Biostatistics, University of Michigan, Ann Arbor, 48109, Michigan, USA
| | - Zhenxing Guo
- School of Data Science, The Chinese University of Hong Kong - Shenzhen, Shenzhen, 518172, Guangdong, China
| | - Hao Feng
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA
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Zhang Y, Wang L, Liu Y, Yan F. Mettl3-mediated transcriptome-wide m6A methylation induced by cigarette smoking in human bronchial epithelial cells. Toxicol In Vitro 2023; 89:105584. [PMID: 36924977 DOI: 10.1016/j.tiv.2023.105584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/17/2023] [Accepted: 03/13/2023] [Indexed: 03/16/2023]
Abstract
Cigarette smoke exposure is a well-recognized causative factor for Chronic obstructive pulmonary disease (COPD), but the molecular mechanisms responsible for this effect need to be further investigated. An expanding number of studies suggest that m6A modification is involved in the progression of various diseases. Nevertheless, evidence on the regulatory function of m6A modification in human bronchial epithelial cells exposed to cigarette smoke is scarce. In this study, we investigated for the first time the effect of cigarette smoke exposure on contributing to high Mettl3 expression in HBE cells in vitro, an essential m6A writer. To investigate the pattern of m6A modification in HBE cells following cigarette smoke exposure, Mettl3 was down-regulated in HBE cells and a MeRIP-seq analysis revealed differences in m6A methylation between wild-type (WT) and Mettl3 knockdown HBE cells exposed to CSE. There were 1584 significantly hypomethylated genes engaged in multicellular organismal developments. We identified 200 differentially expressed genes with hypomethylated m6A peaks in conjunction with Mettl3 knockdown, among four candidate genes (NR1H4, TSPEAR, ACSBG1, and SLC5A5) that could be further explored in COPD. According to the research, cigarette smoke may control the behavior of human bronchial epithelial cells through m6A modification in COPD, providing a unique molecular mechanism.
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Affiliation(s)
- Yaping Zhang
- Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, 34 North Zhongshan Road, Licheng District, Quanzhou, China.
| | - Lixing Wang
- Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, 34 North Zhongshan Road, Licheng District, Quanzhou, China
| | - Yifei Liu
- Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, 34 North Zhongshan Road, Licheng District, Quanzhou, China
| | - Furong Yan
- Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, 34 North Zhongshan Road, Licheng District, Quanzhou, China
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23
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Li Z, Zhang L, Jiang Y, Lin X, Liao Y, Yang B, Teng M. Transcriptome-wide assessment of N6-methyladenosine modification identifies different gene expression and infection-associated pathways in Treponema pallidum-infected macrophage. J Dermatol Sci 2023:S0923-1811(23)00060-9. [PMID: 36841722 DOI: 10.1016/j.jdermsci.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 12/18/2022] [Accepted: 02/16/2023] [Indexed: 02/21/2023]
Abstract
BACKGROUND Treponema pallidum (Tp) is a widespread and destructive pathogen that leads to syphilis. As the acknowledged executor of host immunity, macrophage plays vital roles in combating the invasion and migration of Tp. However, the mechanisms of these processes are largely unknown, especially the critical driver genes and associated modifications. OBJECTIVE We aimed to systematically dissect the global N6-methyladenosine (m6A) RNA modification patterns in Tp-infected macrophages. METHODS The RNA of Tp-infected/non-infected macrophage was extracted, followed by mRNA sequencing and methylated RNA immunoprecipitation (MeRIP) sequencing. Bioinformatics analysis was executed by m6A peaks and motifs identification, Gene ontology and signaling pathways analysis of differentially expressed genes, and comprehensive comparison. The m6A levels were measured by RNA Methylation Assay, and m6A modified genes were determined by qPCR. RESULTS Totally, 2623 unique and 3509 common m6A peaks were proved along with related transcripts in Tp-infected macrophages. The common m6A-related genes were enriched in the signals of oxidative stress, cell differentiation, and angiogenesis, while unique genes in those of metabolism, inflammation, and infection. And differentially expressed transcripts revealed various biological processes and pathways associated with catabolic and infection. They also experienced comprehensive analysis due to hyper-/hypo-methylation. And the m6A level of macrophage was elevated, along with qPCR validation of specific genes. CONCLUSION With a particular m6A transcriptome-wide map, our study provides unprecedented insights into the RNA modification of macrophage stimulated by Tp in vitro, which partially differs from other infections and may provide clues to explore the immune process for syphilis.
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Zhu L, Liu S, Liao F, Yang J, Liang T, Yang Y, Huang X, Gu L, Su L. Comprehensive Analysis of Blood-Based m6A Methylation in Human Ischemic Stroke. Mol Neurobiol 2023; 60:431-446. [PMID: 36279101 DOI: 10.1007/s12035-022-03064-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/03/2022] [Indexed: 01/21/2023]
Abstract
Alterations of N6-methyladenosine (m6A) methylation have been reported in the cerebral cortices of mouse and rat models of ischemic stroke (IS). However, the role of m6A methylation in human IS is still unknown. We assessed m6A levels in peripheral blood from patients with IS and healthy controls. A transient middle cerebral artery occlusion and reperfusion (tMCAO/R) mouse model, and an oxygen-glucose deprivation/reperfusion (OGD/R) model in A172 cells were established to further assess m6A levels. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing were performed in the peripheral blood of patients with IS and healthy controls. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to identify underlying biological processes. In this study, we found that global m6A levels were elevated in the peripheral blood of patients with IS, in the cerebral cortex of mice after tMCAO/R treatment and in A172 cells after OGD/R treatment. MeRIP-seq analysis identified 2115 altered m6A peaks in patients with IS, 1052 upregulated and 1063 downregulated. Downregulated methylated mRNAs were enriched in Hippo signaling pathway, cytokine-cytokine receptor interaction, NF-kappa B signaling pathway, etc. Upregulated methylated mRNAs were enriched in calcium signaling pathways, Hedgehog signaling pathway, MAPK signaling pathway, etc. Moreover, a total of 84 differentially expressed mRNAs with altered m6A peaks were identified and enriched in EGFR tyrosine kinase inhibitor, Hematopoietic cell lineage, and cytokine-cytokine receptor interactions. This study is the first to profile the transcriptome-wide m6A methylome of peripheral blood in human IS and uncover increased global m6A levels in the peripheral blood of patients with IS.
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Affiliation(s)
- Lulu Zhu
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi, China
| | - Shengying Liu
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi, China
| | - Fangping Liao
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi, China
| | - Jialei Yang
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi, China
| | - Tian Liang
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi, China
| | - Yibing Yang
- Department of Internal Neurology, First Affiliated Hospital, Guangxi University of Chinese Medicine, 89-9 Dongge Road, Nanning, Guangxi, China
| | - Xianli Huang
- Department of Internal Neurology, First Affiliated Hospital, Guangxi University of Chinese Medicine, 89-9 Dongge Road, Nanning, Guangxi, China
| | - Lian Gu
- Department of Internal Neurology, First Affiliated Hospital, Guangxi University of Chinese Medicine, 89-9 Dongge Road, Nanning, Guangxi, China.
| | - Li Su
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi, China.
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25
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Li J, Ding J, Chen M, Chen K, Zou Y, Xu X, Zhang D, Yu X, Ding Z. Transcriptome-wide N6-methyladenosine modification profiling of mRNAs during infection of Newcastle disease virus in chicken macrophages. Virus Res 2023; 323:198993. [PMID: 36326508 PMCID: PMC10194374 DOI: 10.1016/j.virusres.2022.198993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/15/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
N6-methyladenosine (m6A) modification, the most prevalent post-transcriptional modification of eukaryotic mRNAs, is reported to play a crucial role in viral infection. However, the role of m6A modification during Newcastle disease virus (NDV) infection has remained unclear. In this study, we performed MeRIP-seq to investigate the transcriptome-wide m6A methylome and m6A-modified genes in NDV-infected chicken macrophages. A total of 9496 altered peaks were identified, of which 7015 peaks were significantly upregulated across 3320 genes, and 2481 peaks were significantly down-regulated across 1264 genes. Combined analysis of m6A peaks and mRNA expression showed that 1234 mRNAs had significantly altered levels of methylation and expression after NDV infection, and m6A modification tended to have a negative relationship with mRNA expression, suggesting that m6A modification may regulate the process of NDV infection by regulating gene expression, particularly of the genes important in the innate immune response. To the best of our knowledge, this is the first comprehensive characterization of m6A patterns in chicken macrophage mRNA after NDV infection, providing a valuable basis for further exploring the role of m6A modification mechanisms during the course of NDV infection.
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Affiliation(s)
- Jindou Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Jiaxin Ding
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Minghua Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Kainan Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yinxue Zou
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xiaohong Xu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Di Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xibing Yu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zhuang Ding
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
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Guo Z, Shafik AM, Jin P, Wu Z, Wu H. Analyzing mRNA Epigenetic Sequencing Data with TRESS. Methods Mol Biol 2023; 2624:163-183. [PMID: 36723816 DOI: 10.1007/978-1-0716-2962-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
RNA epigenetics has emerged as an active topic to study gene regulation mechanisms. In this regard, the MeRIP-seq technology allows profiling transcriptome-wide mRNA modifications, in particular m6A. The primary goals for the analysis of MeRIP-seq data are the identification of m6A-methylated regions under each condition and across different biological conditions. Here we describe detailed procedures to guide researchers in MeRIP-seq data analyses by providing step-by-step instructions of the dedicated bioconductor package TRESS.
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Affiliation(s)
- Zhenxing Guo
- Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Andrew M Shafik
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Zhijin Wu
- Department of Biostatistics, Brown University, Providence, RI, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA, USA.
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Lin Y, Zhao Z, Nie W, Huang M, Cai J, Wang Y, Wang H, Huang Y, Bai Y. Overview of distinct 5-methylcytosine profiles of messenger RNA in normal and knock-down NSUN2 colorectal cancer cells. Front Genet 2023; 14:1121063. [PMID: 37168511 PMCID: PMC10166136 DOI: 10.3389/fgene.2023.1121063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 04/10/2023] [Indexed: 05/13/2023] Open
Abstract
Background: Colorectal cancer (CRC) is a harmful cancer with high morbidity and poor prognosis. There is growing evidence that RNA methylation is closely related to the occurrence of cancer and its malignant biological behavior. N6-methyladenosine (m6A) methylation is the most common RNA modification in eukaryotes, and its multiple regulatory mechanisms in CRC have been elucidated from multiple perspectives. At the same time, the role of 5-methylcytosine (m5C), another important and widely distributed methylation modification, in CRC is far from being elucidated. Methods: In this study, we used RNA immunoprecipitation sequencing combined with bioinformatics methods to identify the m5C peaks on messenger RNA (mRNA) in HCT15 cells and sh-NSUN2 HCT15 cells, understand which transcripts are modified by m5C, and characterize the distribution of m5C modifications. In addition, we performed further bioinformatics analysis of the detected data to initially clarify the potential function of these m5C-modified transcripts. Results: We found significant differences in the distribution of m5C between HCT15 cells and sh-NSUN2 HCT15 cells, suggesting that m5C is likely to play a key role in the occurrence and development of CRC. Furthermore, Gene Ontology (GO) enrichment analysis showed that genes altered by m5C were mainly enriched in phylogeny, synaptic membrane, and transcription factor binding. The Kyoto Encyclopedia of Genes and Genomes (KEGG)pathway analysis showed that the genes altered by m5C are enriched in ECM receptor interaction pathway, the circadian pathway, and the cAMP signaling pathway. Conclusion: Here, our study preliminarily revealed the different distribution patterns of m5C between HCT15 cell and sh-NSUN2 HCT15 cell. Our results open a new window to understand the role of m5C RNA methylation of mRNA in the development of CRC.
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Affiliation(s)
- Yu Lin
- Department Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nan Fang Hospital, Southern Medical University, Guangzhou, China
- Department of Gastroenterology, Baiyun Branch, Nan Fang Hospital, Southern Medical University, Guangzhou, China
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Yu Lin, ; Yongmei Huang, ; Yang Bai,
| | - Zhifang Zhao
- Department Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nan Fang Hospital, Southern Medical University, Guangzhou, China
| | - Wenqiang Nie
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Manting Huang
- Department of Vascular Intervention, Zhongshan Hospital of Traditional Chinese Medicine, Affiliated to Guangzhou University of Chinese Medicine, Zhongshan, China
| | - Jiazhong Cai
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yadong Wang
- Department Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nan Fang Hospital, Southern Medical University, Guangzhou, China
| | - Hesong Wang
- Department of Gastroenterology, Baiyun Branch, Nan Fang Hospital, Southern Medical University, Guangzhou, China
| | - Yongmei Huang
- Department of Gastroenterology, Baiyun Branch, Nan Fang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Yu Lin, ; Yongmei Huang, ; Yang Bai,
| | - Yang Bai
- Department Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nan Fang Hospital, Southern Medical University, Guangzhou, China
- Department of Gastroenterology, Baiyun Branch, Nan Fang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Yu Lin, ; Yongmei Huang, ; Yang Bai,
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Li W, Xing C, Bao L, Han S, Luo T, Wang Z, Fan H. Comprehensive analysis of RNA m6A methylation in pressure overload-induced cardiac hypertrophy. BMC Genomics 2022; 23:576. [PMID: 35953789 PMCID: PMC9373449 DOI: 10.1186/s12864-022-08833-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022] Open
Abstract
Aim To analyze and compare the mRNA N6-methyladenosine modifications in transverse aortic constriction induced mice hearts and normal mice hearts. Materials and methods Colorimetric quantification was used to probe the changes in m6A modifications in the total RNA. The expression of m6A-related enzymes was analyzed via qRT-PCR and western blotting. RNA-seq and MeRIP-seq were performed to identify genes with differences in m6A modifications or expression in the transcriptome profile. Results Compared with the control group, the TAC group exhibited higher m6A methylation levels. FTO and WTAP were downregulated after TAC, while METTL3 was significantly downregulated at the protein level. MeRIP-seq revealed that 1179 m6A peaks were upmethylated and 733 m6A peaks were downmethylated, and biological analysis of these genes exhibited a strong relationship with heart function. Conclusion Our findings provide novel information regarding m6A modification and gene expression changes in cardiac hypertrophy, which may be fundamental for further research. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08833-w.
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Affiliation(s)
- Weidong Li
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, No.100 Kexuedadao Road, Zhengzhou, 450000, China
| | - Chenxv Xing
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, No.100 Kexuedadao Road, Zhengzhou, 450000, China
| | - Limeng Bao
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, No.100 Kexuedadao Road, Zhengzhou, 450000, China
| | - Shengna Han
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, No.100 Kexuedadao Road, Zhengzhou, 450000, China
| | - Tianxia Luo
- Department of Physiology, School of Medicine, Henan University of Chinese Medicine, No.156 Jinshui Road, Zhengzhou, 450052, China
| | - Zhiju Wang
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, No.100 Kexuedadao Road, Zhengzhou, 450000, China
| | - Hongkun Fan
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, No.100 Kexuedadao Road, Zhengzhou, 450000, China.
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Song J, Zeng Y, Zhu M, Zhu G, Chen C, Jin M, Wang J, Song Y. Comprehensive analysis of transcriptome-wide m 6A methylome in the lung tissues of mice with acute particulate matter exposure. Ecotoxicol Environ Saf 2022; 241:113810. [PMID: 35777340 DOI: 10.1016/j.ecoenv.2022.113810] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/06/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Particulate matter (PM) exposure is identified as a critical risk factor for chronic airway diseases, but the biological mechanism of PM-induced lung damage was not fully elucidated. The m6A methylation, as the main member of epigenetic modifications, has been found to play an important role in different pulmonary diseases, but its regulatory effect on PM-induced lung damage remains unknown. This study firstly used the methylated RNA immunoprecipitation sequencing (MeRIP-seq) to reveal the m6A methylome profiles in the lung tissues of mice with acute PM exposure. Compared with the normal control, a total of 2210 differentially hypermethylated m6A peaks within 1879 genes and 1278 differentially hypomethylated m6A peaks within 1153 genes were identified in the PM-exposed group. Conjoint analysis of MeRIP-seq and high-throughput sequencing for RNA (RNA-seq) data predicated several potential pathways including MAPK signaling pathway, cell senescence, and cell cycle. Four m6A-modified differentially expressed genes (IL-1a, IL-1b, ADAM-8, and HMOX-1) were selected for validation using MeRIP-qPCR. Furthermore, the m6A-modified IL-1a promoted PM-induced inflammation via regulating MAPK signaling pathway. These results provide a new insight into the biological mechanism of PM-induced lung damage, and help us to develop new methods to prevent and treat PM-induced adverse health effects.
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Affiliation(s)
- Juan Song
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Yingying Zeng
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Mengchan Zhu
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Guiping Zhu
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Cuicui Chen
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Meiling Jin
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Jian Wang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200030, China.
| | - Yuanlin Song
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200030, China
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She J, Tan K, Liu J, Cao S, Li Z, Peng Y, Xiao Z, Diao R, Wang L. The Alteration of m 6A Modification at the Transcriptome-Wide Level in Human Villi During Spontaneous Abortion in the First Trimester. Front Genet 2022; 13:861853. [PMID: 35754822 PMCID: PMC9215105 DOI: 10.3389/fgene.2022.861853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
A growing number of studies have demonstrated that N6 methyladenine (m6A) acts as an important role in the pathogenesis of reproductive diseases. Therefore, it is essential to profile the genome-wide m6A modifications such as in spontaneous abortion. In this study, due to the trace of human villi during early pregnancy, we performed high-throughput sequencing in villous tissues from spontaneous abortion (SA group) and controls with induced abortion (normal group) in the first trimester. Based on meRIP-seq data, 18,568 m6A peaks were identified. These m6A peaks were mainly located in the coding region near the stop codon and were mainly characterized by AUGGAC and UGGACG motif. Compared with normal group, the SA group had 2,159 significantly upregulated m6A peaks and 281 downregulated m6A peaks. Biological function analyses revealed that differential m6A-modified genes were mainly involved in the Hippo and Wnt signaling pathways. Based on the conjoint analysis of meRIP-seq and RNA-seq data, we identified thirty-five genes with differentially methylated m6A peaks and synchronously differential expression. And these genes were mainly involved in the Wnt signaling pathway, phosphatase activity regulation, protein phosphatase inhibitor activity, and transcription inhibitor activity. This study is the first to profile the transcriptome-wide m6A methylome in spontaneous abortion during early pregnancy, which provide novel insights into the pathogenesis and treatment of spontaneous abortion in the first trimester.
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Affiliation(s)
- Jiajie She
- The First Affiliated Hospital of Shenzhen University, Reproductive Medicine Centre, Shenzhen Second People's Hospital, Shenzhen, China.,Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Kaifen Tan
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jie Liu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shuo Cao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zengguang Li
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - You Peng
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhuoyu Xiao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ruiying Diao
- The First Affiliated Hospital of Shenzhen University, Reproductive Medicine Centre, Shenzhen Second People's Hospital, Shenzhen, China
| | - Liping Wang
- The First Affiliated Hospital of Shenzhen University, Reproductive Medicine Centre, Shenzhen Second People's Hospital, Shenzhen, China
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Guo S, Wang X, Cao M, Wu X, Xiong L, Bao P, Chu M, Liang C, Yan P, Pei J, Guo X. The transcriptome-wide N6-methyladenosine (m 6A) map profiling reveals the regulatory role of m 6A in the yak ovary. BMC Genomics 2022; 23:358. [PMID: 35538402 PMCID: PMC9092806 DOI: 10.1186/s12864-022-08585-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 04/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND AND AIM Yak estrus is a seasonal phenomenon, probably involving epigenetic regulation of synthesis and secretion of sex hormones as well as growth and development of follicles. N6-methyladenosine (m6A) is the most common internal modification of the eukaryotic mRNA. However, there are no detailed reports on the m6A transcriptome map of yak ovary. Therefore, this study aimed to collected the yak ovarian tissues at three different states of anestrus (YO-A), estrus (YO-F), and pregnancy (YO-P), and obtained the full transcriptome m6A map in yak by MeRIP-seq. RESULTS The HE staining revealed that the number of growing follicles and mature follicles in the ovary during the estrus period was relatively higher than those in the anestrus period and the pregnancy period. The RT-qPCR showed that the expression of METTL3, METTL14, FTO, YTHDC1 were significantly different across different periods in the ovaries, which suggests that m6A may play a regulatory role in ovarian activity. Next, we identified 20,174, 19,747 and 13,523 m6A peaks in the three ovarian samples of YO-A, YO-F and YO-P using the methylated RNA immunoprecipitation sequencing (MeRIP-seq). The m6A peaks are highly enriched in the coding sequence (CDS) region and 3'untranslated region (3'UTR) as well as the conserved sequence of "RRACH." The GO, KEGG and GSEA analysis revealed the involvement of m6A in many physiological activities of the yak's ovary during reproductive cycle. The association analysis found that some genes such as BNC1, HOMER1, BMP15, BMP6, GPX3, and WNT11 were related to ovarian functions. CONCLUSIONS The comparison of the distribution patterns of methylation peaks in the ovarian tissues across different periods further explored the m6A markers related to the regulation of ovarian ovulation and follicular development in the yak ovary. This comprehensive map provides a solid foundation for revealing the potential function of the mRNA m6A modification in the yak ovary.
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Affiliation(s)
- Shaoke Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Xingdong Wang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Mengli Cao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Lin Xiong
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
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Yang L, Chen X, Qian X, Zhang J, Wu M, Yu A. Comprehensive Analysis of the Transcriptome-Wide m6A Methylome in Endometrioid Ovarian Cancer. Front Oncol 2022; 12:844613. [PMID: 35280730 PMCID: PMC8904756 DOI: 10.3389/fonc.2022.844613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/01/2022] [Indexed: 12/27/2022] Open
Abstract
Emerging studies have revealed that N6-methyladenosine modification is involved in the development of various cancers. However, the m6A modification pattern of endometrioid ovarian cancer (EOC) has not been demonstrated. In the present study, high-throughput sequencing combined with methylated RNA immunoprecipitation (MeRIP-seq) and RNA sequencing were used to obtain the transcriptome-wide m6A modifications of endometrioid ovarian cancer for the first time. The roles of methyltransferase-like 3 (METTL3) in EOC cell line COV362 were explored. In total, 39,237 m6A-modified peaks related to 17,082 genes were identified in the EOC group, and 52,848 m6A peaks representing 19,349 genes were detected in endometriosis group. Functional enrichment analysis revealed that m6A enriched genes were associated with tight junctions, cell adhesion molecules, platinum drug resistance, adherens junction, and more. METTL3 knockdown in the COV362 cells significantly decreased cell proliferation, promoted cell apoptosis, and induced cell cycle arrest at the G0/G1 phase. Our study presented the transcriptome-wide m6A modifications of endometrioid ovarian cancer for the first time and revealed various differentially expressed genes with methylated m6A modifications. This study may provide new directions for in-depth research of the underlying molecular mechanisms and signaling pathways of EOC development and progression.
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Affiliation(s)
- Li Yang
- Department of Gynecological Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Xin Chen
- Department of Gynecological Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Xiang Qian
- Department of Traditional Chinese Medicine, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Jiejie Zhang
- Department of Gynecological Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Meijuan Wu
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Aijun Yu
- Department of Gynecological Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
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Han C, Zhang F, Qiao X, Zhao Y, Qiao Q, Huang X, Zhang S. Multi-Omics Analysis Reveals the Dynamic Changes of RNA N 6 -Methyladenosine in Pear ( Pyrus bretschneideri) Defense Responses to Erwinia amylovora Pathogen Infection. Front Microbiol 2022; 12:803512. [PMID: 35222304 PMCID: PMC8867029 DOI: 10.3389/fmicb.2021.803512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/30/2021] [Indexed: 11/21/2022] Open
Abstract
N6-methylated adenine (m6A) is the most prevalent modification of mRNA methylation and can regulate many biological processes in plants, such as mRNA processing, development, and stress response. Some studies have increased our understanding of its various roles in model plants in recent years. Nevertheless, the distribution of m6A and the impact of m6A on the regulation of plant defense responses against pathogen inoculation are virtually unknown in pear. In this study, MeRIP-seq and RNA-seq data from healthy and inoculated plants were analyzed to assess the changes in the transcript levels and posttranscriptional modification of pear in response to the fire blight pathogen Erwinia amylovora. Following the analysis of 97,261 m6A peaks, we found that m6A preferred to modify duplicate genes rather than singleton genes and that m6A-methylated genes underwent stronger purifying selection. A total of 2,935 specific m6A sites were detected at the transcriptome level after inoculation, which may increase defense-related transcript abundance to enhance pear resistance. In addition, 1,850 transcripts were detected only in the mock-inoculated groups. The hypomethylated transcripts were mainly related to transcriptional regulation and various biological processes, such as chloroplast organization and sucrose biosynthetic processes. In addition, we found that the extent of m6A methylation was significantly positively correlated with the transcript level, suggesting a regulatory role for m6A in the plant response.
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Affiliation(s)
- Chenyang Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Feng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xin Qiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yancun Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qinhai Qiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xiaosan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Wang Y, Du F, Li Y, Wang J, Zhao X, Li Z, Xu J, Wang W, Fu B. Global N 6-Methyladenosine Profiling Revealed the Tissue-Specific Epitranscriptomic Regulation of Rice Responses to Salt Stress. Int J Mol Sci 2022; 23:2091. [PMID: 35216209 DOI: 10.3390/ijms23042091] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/29/2022] [Accepted: 02/10/2022] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) methylation represents a new layer of the epitranscriptomic regulation of plant development and growth. However, the effects of m6A on rice responses to environmental stimuli remain unclear. In this study, we performed a methylated-RNA immunoprecipitation sequencing analysis and compared the changes in m6A methylation and gene expression in rice under salt stress conditions. Salt stress significantly increased the m6A methylation in the shoots (p value < 0.05). Additionally, 2537 and 2304 differential m6A sites within 2134 and 1997 genes were identified in the shoots and roots, respectively, under salt stress and control conditions. These differential m6A sites were largely regulated in a tissue-specific manner. A unique set of genes encoding transcription factors, antioxidants, and auxin-responsive proteins had increased or decreased m6A methylation levels only in the shoots or roots under salt stress, implying m6A may mediate salt tolerance by regulating transcription, ROS homeostasis, and auxin signaling in a tissue-specific manner. Integrating analyses of m6A modifications and gene expression changes revealed that m6A changes regulate the expression of genes controlling plant growth, stress responses, and ion transport under saline conditions. These findings may help clarify the regulatory effects of m6A modifications on rice salt tolerance.
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Wu J, Deng LJ, Xia YR, Leng RX, Fan YG, Pan HF, Ye DQ. Involvement of N6-methyladenosine modifications of long noncoding RNAs in systemic lupus erythematosus. Mol Immunol 2022; 143:77-84. [PMID: 35051888 DOI: 10.1016/j.molimm.2022.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/17/2021] [Accepted: 01/11/2022] [Indexed: 12/17/2022]
Abstract
BACKGROUND LncRNAs are potential biomarkers for SLE, but the epigenetic regulatory mechanisms of N6-methyladenosine (m6A) modification in SLE remain largely unclear. METHODS In this study, we established m6A modification profile and investigated the potential roles of m6A-related lncRNAs in SLE. The m6A modification profile of SLE was established using MeRIP-seq. Four potential m6A related-lncRNAs (linc02446, linc01410, Xist, and PSMB8-AS1) were selected for validation using qRT-PCR, and their expression and association with clinical characteristics with SLE were evaluated. RESULTS Overall, m6A level was lower in patients with SLE than in controls. Compared with controls, the expression of the two m6A related-lncRNAs (Xist and PSMB8-AS1) was downregulated in patients with SLE (all P < 0.05); the linc02446 was up-regulated in PBMCs of patients with SLE (Z=-2.738, P = 0.006), while it was not differentially expressed in T cells (Z=-0.387, P = 0.699). No significant alteration in linc01410 expression was observed in patients (Z=-0.940, P = 0.347). The lower expression levels of Xist and PSMB8-AS1 were associated with many clinical manifestations in patients with SLE (all P < 0.05). Additionally, mRNAs co-expressed with m6A related-lncRNAs (Xist, linc02446, and PSMB8-AS1) also participated in SLE. CONCLUSION These results suggest that m6A methylation and m6A related-lncRNAs might be involved in the pathogenesis of SLE. Thus, our findings provide some clues on the potential function of lncRNAs that m6A modification may target in novel therapeutic or diagnostic strategies for SLE.
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Affiliation(s)
- Jun Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Li-Jun Deng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Yuan-Rui Xia
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Rui-Xue Leng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Yin-Guang Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Dong-Qing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China.
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Zhang Y, Liang C, Wu X, Pei J, Guo X, Chu M, Ding X, Bao P, Kalwar Q, Yan P. Integrated Study of Transcriptome-wide m 6A Methylome Reveals Novel Insights Into the Character and Function of m 6A Methylation During Yak Adipocyte Differentiation. Front Cell Dev Biol 2021; 9:689067. [PMID: 34926439 PMCID: PMC8678508 DOI: 10.3389/fcell.2021.689067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/01/2021] [Indexed: 12/13/2022] Open
Abstract
Yak (Bos grunniens) is considered an iconic symbol of Tibet and high altitude, but they suffer from malnutrition during the cold season that challenges the metabolism of energy. Adipocytes perform a crucial role in maintaining the energy balance, and adipocyte differentiation is a complex process involving multiple changes in the expression of genes. N 6-methyladenosine (m6A) plays a dynamic role in post-transcription gene expression regulation as the most widespread mRNA modification of the higher eukaryotes. However, currently there is no research existing on the m6A transcriptome-wide map of bovine animals and their potential biological functions in adipocyte differentiation. Therefore, we performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to determine the distinctions in m6A methylation and gene expression during yak adipocyte differentiation. In yak adipocyte and preadipocyte the content of m6A and m6A-associated enzymes was substantially different. In the two groups, a total of 14,710 m6A peaks and 13,388 m6A peaks were identified. For the most part, m6A peaks were enriched in stop codons, 3'-untranslated regions, and coding regions with consensus motifs of GGACU. The functional enrichment exploration displayed that differentially methylated genes participated in some of the pathways associated with adipogenic metabolism, and several candidate genes (KLF9, FOXO1, ZNF395, and UHRF1) were involved in these pathways. In addition to that, there was a positive association between m6A abundance and levels of gene expression, which displayed that m6A may play a vital role in modulating gene expression during yak adipocyte differentiation. Further, in the adipocyte group, several methylation gene protein expression levels were significantly higher than in preadipocytes. In short, it can be concluded that the current study provides a comprehensive explanation of the m6A features in the yak transcriptome, offering in-depth insights into m6A topology and associated molecular mechanisms underlying bovine adipocyte differentiation, which might be helpful for further understanding its mechanisms.
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Affiliation(s)
- Yongfeng Zhang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuezhi Ding
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Qudratullah Kalwar
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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Yang H, Wu YF, Ding J, Liu W, Zhu DS, Shen XF, Guan YT. Comprehensive Analysis of N 6-Methyladenosine (m 6A) Methylation in Neuromyelitis Optica Spectrum Disorders. Front Genet 2021; 12:735454. [PMID: 34899833 PMCID: PMC8660110 DOI: 10.3389/fgene.2021.735454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Background: N6-Methyladenosine (m6A) methylation is the most prevalent internal posttranscriptional modification on mammalian mRNA. But its role in neuromyelitis optica spectrum disorders (NMOSD) is not known. Aims: To explore the mechanism of m6A in NMOSD patients. Methods: This study assessed the m6A methylation levels in blood from two groups: NMOSD patients and healthy controls. Methylated RNA immunoprecipitation Sequencing (MeRIP-seq) and RNA-seq were performed to assess differences in m6A methylation between NMOSD patients and healthy controls. Ultra-high performance liquid chromatography coupled with triple quadruple mass spectrometry (UPLC-QQQ-MS) method was performed to check m6A level. Differential m6A methylation genes were validated by MeRIP-qPCR. Results: Compared with that in the control group, the total m6A level was decreased in the NMOSD group. Genes with upregulated methylation were primarily enriched in processes associated with RNA splicing, mRNA processing, and innate immune response, while genes with downregulated methylation were enriched in processes associated with the regulation of transcription, DNA-templating, and the positive regulation of I-kappa B kinase/NF-kappa B signalling. Conclusion: These findings demonstrate that differential m6A methylation may act on functional genes to regulate immune homeostasis in NMOSD.
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Affiliation(s)
- Hong Yang
- Department of Neurology, The First Rehabilitation Hospital of Shanghai, Tongji University School of Medicine, Shanghai, China
| | - Yi-Fan Wu
- Department of Neurology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Ding
- Department of Neurology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Liu
- Department of Neurology, The First Rehabilitation Hospital of Shanghai, Tongji University School of Medicine, Shanghai, China
| | - De-Sheng Zhu
- Department of Neurology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xia-Feng Shen
- Department of Neurology, The First Rehabilitation Hospital of Shanghai, Tongji University School of Medicine, Shanghai, China
| | - Yang-Tai Guan
- Department of Neurology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of Neurology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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Yang J, Yang Q, Zhang J, Gao X, Luo R, Xie K, Wang W, Li J, Huang X, Yan Z, Wang P, Gun S. N6-Methyladenosine Methylation Analysis of Long Noncoding RNAs and mRNAs in IPEC-J2 Cells Treated With Clostridium perfringens beta2 Toxin. Front Immunol 2021; 12:769204. [PMID: 34880865 PMCID: PMC8646102 DOI: 10.3389/fimmu.2021.769204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
Background The n6-methyladenosine (m6A) modification is present widely in mRNAs and long non-coding RNAs (lncRNAs), and is related to the occurrence and development of certain diseases. However, the role of m6A methylation in Clostridium perfringens type C infectious diarrhea remains unclear. Methods Here, we treated intestinal porcine jejunum epithelial cells (IPEC-J2 cells) with Clostridium perfringens beta2 (CPB2) toxin to construct an in vitro model of Clostridium perfringens type C (C. perfringens type C) infectious diarrhea, and then used methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to identify the methylation profiles of mRNAs and lncRNAs in IPEC-J2 cells. Results We identified 6,413 peaks, representing 5,825 m6A-modified mRNAs and 433 modified lncRNAs, of which 4,356 m6A modified mRNAs and 221 m6A modified lncRNAs were significantly differential expressed between the control group and CPB2 group. The motif GGACU was enriched significantly in both the control group and the CPB2 group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis showed that the differentially methylated modified mRNAs were mainly enriched in Hippo signaling pathway and Wnt signaling pathway. In addition, the target genes of the differentially m6A modified lncRNAs were related to defense response to virus and immune response. For example, ENSSSCG00000042575, ENSSSCG00000048701 and ENSSSCG00000048785 might regulate the defense response to virus, immune and inflammatory response to resist the harmful effects of viruses on cells. Conclusion In summary, this study established the m6A transcription profile of mRNAs and lncRNAs in IPEC-J2 cells treated by CPB2 toxin. Further analysis showed that m6A-modified RNAs were related to defense against viruses and immune response after CPB2 toxin treatment of the cells. Threem6A-modified lncRNAs, ENSSSCG00000042575, ENSSSCG00000048785 and ENSSSCG00000048701, were most likely to play a key role in CPB2 toxin-treated IPEC-J2 cells. The results provide a theoretical basis for further research on the role of m6A modification in piglet diarrhea.
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Affiliation(s)
- Jiaojiao Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Qiaoli Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Juanli Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoli Gao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ruirui Luo
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Kaihui Xie
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wei Wang
- College of Animal Science and Technology, Northwest A&F University, Xian, China
| | - Jie Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoyu Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zunqiang Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Pengfei Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Gansu Research Center for Swine Production Engineering and Technology, Lanzhou, China
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Liu SY, Wu JJ, Chen ZH, Zou ML, Teng YY, Zhang KW, Li YY, Guo DY, Yuan FL. The m 6A RNA Modification Modulates Gene Expression and Fibrosis-Related Pathways in Hypertrophic Scar. Front Cell Dev Biol 2021; 9:748703. [PMID: 34869335 PMCID: PMC8634666 DOI: 10.3389/fcell.2021.748703] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/22/2021] [Indexed: 12/29/2022] Open
Abstract
Purpose: To systematically analyze the overall m6A modification pattern in hyperplastic scars (HS). Methods: The m6A modification patterns in HS and normal skin (NS) tissues were described by m6A sequencing and RNA sequencing, and subsequently bioinformatics analysis was performed. The m6A-related RNA was immunoprecipitated and verified by real-time quantitative PCR. Results: The appearance of 14,791 new m6A peaks in the HS sample was accompanied by the disappearance of 7,835 peaks. The unique m6A-related genes in HS were thus associated with fibrosis-related pathways. We identified the differentially expressed mRNA transcripts in HS samples with hyper-methylated or hypo-methylated m6A peaks. Conclusion: This study is the first to map the m6A transcriptome of human HS, which may help clarify the possible mechanism of m6A-mediated gene expression regulation.
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Affiliation(s)
- Si-Yu Liu
- Department of Medicine, Institute of Integrated Traditional Chinese and Western Medicine, Wuxi Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Traditional Chinese Medicine, Wuxi, China
| | - Jun-Jie Wu
- Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, China
| | - Zhong-Hua Chen
- Department of Medicine, The Nantong University, Nantong, China
| | - Ming-Li Zou
- Department of Medicine, Institute of Integrated Traditional Chinese and Western Medicine, Wuxi Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Traditional Chinese Medicine, Wuxi, China
| | - Ying-Ying Teng
- The Hospital Affiliated to Jiangnan University, Wuxi, China
| | - Kai-Wen Zhang
- Department of Medicine, Institute of Integrated Traditional Chinese and Western Medicine, Wuxi Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Traditional Chinese Medicine, Wuxi, China
| | - Yue-Yue Li
- The Hospital Affiliated to Jiangnan University, Wuxi, China
| | - Dang-Yang Guo
- The Hospital Affiliated to Jiangnan University, Wuxi, China
| | - Feng-Lai Yuan
- Department of Medicine, Institute of Integrated Traditional Chinese and Western Medicine, Wuxi Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Traditional Chinese Medicine, Wuxi, China.,Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, China.,The Hospital Affiliated to Jiangnan University, Wuxi, China
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40
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Li A, Gan Y, Cao C, Ma B, Zhang Q, Zhang Q, Yao L. Transcriptome-Wide Map of N 6-Methyladenosine Methylome Profiling in Human Bladder Cancer. Front Oncol 2021; 11:717622. [PMID: 34868913 PMCID: PMC8634328 DOI: 10.3389/fonc.2021.717622] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/18/2021] [Indexed: 11/16/2022] Open
Abstract
N6-Methyladenosine (m6A) is the most widespread internal RNA modification in several species. In spite of latest advances in researching the biological roles of m6A, its function in the development and progression of bladder cancer remains unclear. In this study, we used MeRIPty -55-seq and RNA-seq methods to obtain a comprehensive transcriptome-wide m6A profiling and gene expression pattern in bladder cancer and paired normal adjacent tissues. Our findings showed that there were 2,331 hypomethylated and 3,819 hypermethylated mRNAs, 32 hypomethylated and 105 hypermethylated lncRNAs, and 15 hypomethylated and 238 hypermethylated circRNAs in bladder cancer tissues compared to adjacent normal tissues. Furthermore, m6A is most often harbored in the coding sequence (CDS), with some near the start and stop codons between two groups. Functional enrichment analysis revealed that differentially methylated mRNAs, lncRNAs, and circRNAs were mostly enriched in transcriptional misregulation in cancer and TNF signaling pathway. We also found that different m6A methylation levels of gene might regulate its expression. In summary, our results for the first time provide an m6A landscape of human bladder cancer, which expand the understanding of m6A modifications and uncover the regulation of mRNAs, lncRNAs, and circRNAs through m6A modification in bladder cancer.
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Affiliation(s)
- Aolin Li
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Ying Gan
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Congcong Cao
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen-Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Binglei Ma
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Quan Zhang
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Qian Zhang
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Lin Yao
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, China
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Wu J, Yuan XH, Jiang W, Lu YC, Huang QL, Yang Y, Qie HJ, Liu JT, Sun HY, Tang LJ. Genome-wide map of N 6-methyladenosine circular RNAs identified in mice model of severe acute pancreatitis. World J Gastroenterol 2021; 27:7530-7545. [PMID: 34887647 PMCID: PMC8613746 DOI: 10.3748/wjg.v27.i43.7530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/05/2021] [Accepted: 09/16/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Severe acute pancreatitis (SAP) is a deadly inflammatory disease with complex pathogenesis and lack of effective therapeutic options. N6-methyladenosine (m6A) modification of circRNAs plays important roles in physiological and pathological processes. However, the roles of m6A circRNA in the pathological process of SAP remains unknown.
AIM To identify transcriptome-wide map of m6A circRNAs and to determine their biological significance and potential mechanisms in SAP.
METHODS The SAP in C57BL/6 mice was induced using 4% sodium taurocholate salt. The transcriptome-wide map of m6A circRNAs was identified by m6A-modified RNA immunoprecipitation sequencing. The biological significance of circRNAs with differentially expressed m6A peaks was evaluated through gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis. The underlying mechanism of m6A circRNAs in SAP was analyzed by constructing of m6A circRNA-microRNA networks. The expression of demethylases was determined by quantitative polymerase chain reaction and western blot to deduce the possible mechanism of reversible m6A process in SAP.
RESULTS Fifty-seven circRNAs with differentially expressed m6A peaks were identified by m6A-modified RNA immunoprecipitation sequencing, of which 32 were upregulated and 25 downregulated. Functional analysis of these m6A circRNAs in SAP found some important pathways involved in the pathogenesis of SAP, such as regulation of autophagy and protein digestion. In m6A circRNA–miRNA networks, several important miRNAs participated in the occurrence and progression of SAP were found to bind to these m6A circRNAs, such as miR-24-3p, miR-26a, miR-92b, miR-216b, miR-324-5p and miR-762. Notably, the total m6A level of circRNAs was reduced, while the demethylase alkylation repair homolog 5 was upregulated in SAP.
CONCLUSION m6A modification of circRNAs may be involved in the pathogenesis of SAP. Our findings may provide novel insights to explore the possible pathogenetic mechanism of SAP and seek new potential therapeutic targets for SAP.
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Affiliation(s)
- Jun Wu
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu 610036, Sichuan Province, China
- College of Medicine, Southwest Jiaotong University, Chengdu 610036, Sichuan Province, China
| | - Xiao-Hui Yuan
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu 610036, Sichuan Province, China
- College of Medicine, Southwest Jiaotong University, Chengdu 610036, Sichuan Province, China
| | - Wen Jiang
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu 610036, Sichuan Province, China
- College of Medicine, Southwest Jiaotong University, Chengdu 610036, Sichuan Province, China
| | - Yi-Chen Lu
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu 610036, Sichuan Province, China
- College of Medicine, Southwest Jiaotong University, Chengdu 610036, Sichuan Province, China
| | - Qi-Lin Huang
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu 610036, Sichuan Province, China
| | - Yi Yang
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu 610036, Sichuan Province, China
| | - Hua-Ji Qie
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu 610036, Sichuan Province, China
- College of Medicine, Southwest Jiaotong University, Chengdu 610036, Sichuan Province, China
| | - Jiang-Tao Liu
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu 610036, Sichuan Province, China
- College of Medicine, Southwest Jiaotong University, Chengdu 610036, Sichuan Province, China
| | - Hong-Yu Sun
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu 610036, Sichuan Province, China
- College of Medicine, Southwest Jiaotong University, Chengdu 610036, Sichuan Province, China
- Laboratory of Basic Medicine, The General Hospital of Western Theater Command, Chengdu 610036, Sichuan Province, China
| | - Li-Jun Tang
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu 610036, Sichuan Province, China
- College of Medicine, Southwest Jiaotong University, Chengdu 610036, Sichuan Province, China
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Teng F, Tang W, Wuniqiemu T, Qin J, Zhou Y, Huang X, Wang S, Zhu X, Tang Z, Yi L, Wei Y, Dong J. N 6-Methyladenosine Methylomic Landscape of Lung Tissues in Murine Acute Allergic Asthma. Front Immunol 2021; 12:740571. [PMID: 34737744 PMCID: PMC8560743 DOI: 10.3389/fimmu.2021.740571] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
Allergic asthma is well known as a common respiratory disorder comprising an allergic inflammatory nature and excessive immune characteristic. N 6-methyladenosine (m6A) methylation is an RNA epigenetic modification that post-transcriptionally regulates gene expression and function by affecting the RNA fate. Currently, m6A methylation is gaining attention as a mechanism of immunoregulation. However, whether m6A methylation engages the pathological process of asthma remains uncertain. Here, we present the m6A methylomic landscape in the lung tissues of ovalbumin-induced acute asthma mice using MeRIP-seq and RNA-seq. We identified 353 hypermethylated m6A peaks within 329 messenger RNAs (mRNAs) and 150 hypomethylated m6A peaks within 143 mRNAs in the lung tissues of asthmatic mice. These differentially methylated mRNAs were found to be involved in several immune function-relevant signaling pathways. In addition, we predicted 25 RNA-binding proteins that recognize the differentially methylated peak sites by exploring public databases, and the roles of these proteins are mostly related to mRNA biogenesis and metabolism. To further investigate the expression levels of the differentially methylated genes, we performed combined analysis of the m6A methylome and transcriptome data and identified 127 hypermethylated mRNAs (107 high and 20 low expression) and 43 hypomethylated mRNAs with differential expressions (9 high and 34 low expression). Of these, there are a list of mRNAs involved in immune function and regulation. The present results highlight the essential role of m6A methylation in the pathogenesis of asthma.
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Affiliation(s)
- Fangzhou Teng
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Weifeng Tang
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Tulake Wuniqiemu
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Jingjing Qin
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Yaolong Zhou
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Xi Huang
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Shiyuan Wang
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Xueyi Zhu
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Zhao Tang
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - La Yi
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Ying Wei
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Jingcheng Dong
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
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Sun W, Song Y, Xia K, Yu L, Huang X, Zhao Z, Liu J. Transcriptome-wide m 6A methylome during osteogenic differentiation of human adipose-derived stem cells. Stem Cell Res Ther 2021; 12:489. [PMID: 34470673 PMCID: PMC8411547 DOI: 10.1186/s13287-021-02508-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023] Open
Abstract
Objectives Adipose-derived stem cells are frequently used for bone regeneration both in vitro and in vivo. N6-methyladenosine (m6A) is the most abundant post-transcriptional modification on eukaryotic RNAs and plays multifaceted roles in development and diseases. However, the regulatory mechanisms of m6A in osteogenic differentiation of human adipose-derived stem cells (hASCs) remain elusive. The present study aimed to build the transcriptome-wide m6A methylome during the osteogenic differentiation of hASCs. Materials and methods hASCs were harvested after being cultured in a basic or osteogenic medium for 7 days, and the osteogenic differentiation was validated by alkaline phosphatase (ALP) and Alizarin Red S staining, ALP activity assay, and qRT-PCR analysis of ALP, RUNX2, BGLAP, SPP1, SP7, and COL1A1 genes. The m6A level was colorimetrically measured, and the expression of m6A regulators was confirmed by qRT-PCR and western blot. Moreover, m6A MeRIP-seq and RNA-seq were performed to build the transcriptome and m6A methylome. Furthermore, bioinformatic analyses including volcano plots, Venn plots, clustering analysis, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, gene sets enrichment analysis, and protein-protein interaction analysis were conducted. Results In total, 1145 differentially methylated peaks, 2261 differentially expressed genes, and 671 differentially methylated and expressed genes (DMEGs) were identified. GO and KEGG pathway analyses conducted for these DMEGs revealed extensive and osteogenic biological functions. The “PI3K-Akt signaling pathway”; “MAPK signaling pathway”; “parathyroid hormone synthesis, secretion, and action”; and “p53 signaling pathway” were significantly enriched, and the DMEGs in these pathways were identified as m6A-specific key genes. A protein-protein interaction network based on DMEGs was built, and VEGFA, CD44, MMP2, HGF, and SPARC were speculated as the hub DMEGs. Conclusions The total m6A level was reduced with osteogenic differentiation of hASCs. The transcriptome-wide m6A methylome built in the present study indicated quite a few signaling pathways, and hub genes were influenced by m6A modification. Future studies based on these epigenetic clues could promote understanding of the mechanisms of osteogenic differentiation of hASCs. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02508-1.
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Affiliation(s)
- Wentian Sun
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China
| | - Yidan Song
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China
| | - Kai Xia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China
| | - Liyuan Yu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China
| | - Xinqi Huang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China
| | - Zhihe Zhao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China
| | - Jun Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China. .,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041, Sichuan, China.
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Qin Z, Wang W, Ali MA, Wang Y, Zhang Y, Zhang M, Zhou G, Yang JD, Zeng C. Transcriptome-wide m 6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation. BMC Genomics 2021; 22:588. [PMID: 34344298 PMCID: PMC8335898 DOI: 10.1186/s12864-021-07904-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/21/2021] [Indexed: 12/12/2022] Open
Abstract
Background Cryopreservation induces transcriptomic and epigenetic modifications that strongly impairs sperm quality and function, and thus decrease reproductive performance. N6-methyladenosine (m6A) RNA methylation varies in response to stress and has been implicated in multiple important biological processes, including post-transcriptional fate of mRNA, metabolism, and apoptosis. This study aimed to explore whether cryopreservation induces m6A modification of mRNAs associated with sperm energy metabolism, cryoinjuries, and freezability. Results The mRNA and protein expression of m6A modification enzymes were significantly dysregulated in sperm after cryopreservation. Furthermore, m6A peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. The mRNAs containing highly methylated m6A peaks (fts vs. fs) were significantly associated with metabolism and gene expression, while the genes with less methylated m6A peaks were primarily involved in processes regulating RNA metabolism and transcription. Furthermore, the joint analysis of DMMGs and differentially expressed genes indicated that both of these play a vital role in sperm energy metabolism and apoptosis. Conclusions Our study is the first to reveal the dynamic m6A modification of mRNAs in boar sperm during cryopreservation. These epigenetic modifications may affect mRNA expression and are closely related to sperm motility, apoptosis, and metabolism, which will provide novel insights into understanding of the cryoinjuries or freezability of boar sperm during cryopreservation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07904-8.
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Affiliation(s)
- Ziyue Qin
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Wencan Wang
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Malik Ahsan Ali
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China.,Department of Theriogenology, Riphah College of Veterinary Sciences, 54000, Lahore, Pakistan
| | - Yihan Wang
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Yan Zhang
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Ming Zhang
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Guangbin Zhou
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Jian-Dong Yang
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Changjun Zeng
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China. .,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China.
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Abstract
While over 150 distinct types of chemical modifications are known to occur on various cellular RNAs and can be dynamically controlled, the function of most of these modifications remains poorly defined. Collectively, these RNA modifications have been recently termed the "epitranscriptome". Identification and annotation of individual RNA modifications throughout the transcriptome are key for studying the role of the epitranscriptome in the regulation of gene expression and for elucidating the functional relevance of particular RNA modifications in diverse physiological and disease processes. In this protocol, we demonstrate how to identify and annotate RNA modifications based on the informatic analysis of methylated RNA immunoprecipitation and sequencing (MeRIP-seq) data, using RNAmod, a convenient one-stop online interactive platform for the annotation, analysis, and visualization of mRNA modifications.
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46
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Li T, Lin C, Zhu Y, Xu H, Yin Y, Wang C, Tang X, Song T, Guo A, Chen Y, Hu C. Transcriptome Profiling of m 6A mRNA Modification in Bovine Mammary Epithelial Cells Treated with Escherichia coli. Int J Mol Sci 2021; 22:ijms22126254. [PMID: 34200743 PMCID: PMC8230414 DOI: 10.3390/ijms22126254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 01/19/2023] Open
Abstract
Mastitis is a common disease in dairy cows that is mostly caused by E. coli, and it brings massive losses to the dairy industry. N6-Methyladenosine (m6A), a methylation at the N6 position of RNA adenine, is a type of modification strongly associated with many diseases. However, the role of m6A in mastitis has not been investigated. In this study, we used MeRIP-seq to sequence the RNA of bovine mammary epithelial cells treated with inactivated E. coli for 24 h. In this in vitro infection model, there were 16,691 m6A peaks within 7066 mRNA transcripts in the Con group and 10,029 peaks within 4891 transcripts in the E. coli group. Compared with the Con group, 474 mRNAs were hypermethylated and 2101 mRNAs were hypomethylated in the E. coli group. Biological function analyses revealed differential m6A-modified genes mainly enriched in the MAPK, NF-κB, and TGF-β signaling pathways. In order to explore the relationship between m6A and mRNA expression, combined MeRIP-seq and mRNA-seq analyses revealed 212 genes with concomitant changes in the mRNA expression and m6A modification. This study is the first to present a map of RNA m6A modification in mastitis treated with E. coli, providing a basis for future research.
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Affiliation(s)
- Ting Li
- Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (T.L.); (C.L.); (H.X.); (Y.Y.); (C.W.); (X.T.)
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (A.G.); (Y.C.)
| | - Changjie Lin
- Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (T.L.); (C.L.); (H.X.); (Y.Y.); (C.W.); (X.T.)
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (A.G.); (Y.C.)
| | - Yifan Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (A.G.); (Y.C.)
- Department of Preventive Veterinary Medicine, Faculty of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Haojun Xu
- Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (T.L.); (C.L.); (H.X.); (Y.Y.); (C.W.); (X.T.)
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (A.G.); (Y.C.)
| | - Yiya Yin
- Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (T.L.); (C.L.); (H.X.); (Y.Y.); (C.W.); (X.T.)
| | - Chaohao Wang
- Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (T.L.); (C.L.); (H.X.); (Y.Y.); (C.W.); (X.T.)
| | - Xin Tang
- Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (T.L.); (C.L.); (H.X.); (Y.Y.); (C.W.); (X.T.)
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (A.G.); (Y.C.)
| | - Tongxing Song
- Department of Animal Nutrition and Feed Science College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (A.G.); (Y.C.)
- Department of Preventive Veterinary Medicine, Faculty of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingyu Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (A.G.); (Y.C.)
- Department of Preventive Veterinary Medicine, Faculty of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Changmin Hu
- Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (T.L.); (C.L.); (H.X.); (Y.Y.); (C.W.); (X.T.)
- Correspondence: ; Tel.: +86-153-2719-7602
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Han Z, Yang B, Wang Q, Hu Y, Wu Y, Tian Z. Comprehensive analysis of the transcriptome-wide m 6A methylome in invasive malignant pleomorphic adenoma. Cancer Cell Int 2021; 21:142. [PMID: 33653351 PMCID: PMC7923655 DOI: 10.1186/s12935-021-01839-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
Background Invasive malignant pleomorphic adenoma (IMPA) is a highly invasive parotid gland tumor and lacks effective therapy. N6-Methyladenosine (m6A) is the most prevalent post-transcriptional modification of mRNAs in eukaryotes and plays an important role in the pathogenesis of multiple tumors. However, the significance of m6A-modified mRNAs in IMPA has not been elucidated to date. Hence, in this study, we attempted to profile the effect of IMPA in terms of m6A methylation in mRNA. Methods Methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were utilized to acquire the first transcriptome-wide profiling of the m6A methylome map in IMPA followed by bioinformatics analysis. Results In this study, we obtained m6A methylation maps of IMPA samples and normal adjacent tissues through MeRIP-seq. In total, 25,490 m6A peaks associated with 13,735 genes were detected in the IMPA group, whereas 33,930 m6A peaks associated with 18,063 genes were detected in the control group. Peaks were primarily enriched within coding regions and near stop codons with AAACC and GGAC motifs. Moreover, functional enrichment analysis demonstrated that m6A-containing genes were significantly enriched in cancer and metabolism relevant pathways. Furthermore, we identified a relationship between the m6A methylome and the RNA transcriptome, indicating a mechanism by which m6A modulates gene expression. Conclusions Our study is the first to provide comprehensive and transcriptome-wide profiles to determine the potential roles played by m6A methylation in IMPA. These results may open new avenues for in-depth research elucidating the m6A topology of IMPA and the molecular mechanisms governing the formation and progression of IMPA.
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Affiliation(s)
- Zhenyuan Han
- Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.,National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
| | - Biao Yang
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, 200040, China
| | - Qin Wang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yuhua Hu
- Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yuqiong Wu
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China. .,Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
| | - Zhen Tian
- Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
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48
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Wang J, Wang K, Liu W, Cai Y, Jin H. m6A mRNA methylation regulates the development of gestational diabetes mellitus in Han Chinese women. Genomics 2021; 113:1048-1056. [PMID: 33667648 DOI: 10.1016/j.ygeno.2021.02.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 01/20/2021] [Accepted: 02/28/2021] [Indexed: 11/27/2022]
Abstract
N6-methyladenosine (m6A) is the most prevalent mRNA modification in mammals. However, m6A modification profiling and its potential role in gestational diabetes mellitus (GDM) have not yet been investigated. In this work, we performed comprehensive m6A analysis in placental tissues from GDM and control patients to elucidate the role of m6A in GDM. An m6A RNA profile identified that m6A levels were strongly decreased in 3'-untranslated regions (UTRs) and coding sequences (CDSs) near stop codons in GDM placenta samples. Among the many methylated mRNAs, MazF-qPCR verified that the m6A levels of the BAMBI 3'-UTR and CDS were significantly decreased in GDM. BAMBI mRNA and protein expression was significantly decreased in GDM, suggesting that m6A plays a key role in regulating gene expression. In addition, it was verified that the m6A levels of GDM related genes (INSR and IRS1) were significantly reduced in GDM. Taken together, our data suggest that down-regulation of m6A both in the 3'-UTR and CDS near stop codons of placental mRNAs is involved in GDM development in Han Chinese women.
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Affiliation(s)
- Jin Wang
- Prenatal Diagnosis Center, Jinan Maternal and Child Health Care Hospital, Jinan, Shandong Province, PR China
| | - Ke Wang
- Psychology Department, Heze Third People's Hospital, Heze, Shandong Province, PR China
| | - Wei Liu
- Anesthesiology Department, Jinan Maternal and Child Health Care Hospital, Jinan, Shandong Province, PR China
| | - Yan Cai
- Prenatal Diagnosis Center, Jinan Maternal and Child Health Care Hospital, Jinan, Shandong Province, PR China
| | - Hua Jin
- Prenatal Diagnosis Center, Jinan Maternal and Child Health Care Hospital, Jinan, Shandong Province, PR China.
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49
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Cheng B, Leng L, Li Z, Wang W, Jing Y, Li Y, Wang N, Li H, Wang S. Profiling of RNA N 6 -Methyladenosine Methylation Reveals the Critical Role of m 6A in Chicken Adipose Deposition. Front Cell Dev Biol 2021; 9:590468. [PMID: 33614638 PMCID: PMC7892974 DOI: 10.3389/fcell.2021.590468] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
One of the main objectives of broiler breeding is to prevent excessive abdominal adipose deposition. The role of RNA modification in adipose deposition is not clear. This study was aimed to map m6A modification landscape in chicken adipose tissue. MeRIP-seq was performed to compare the differences in m6A methylation pattern between fat and lean broilers. We found that start codons, stop codons, coding regions, and 3′-untranslated regions were generally enriched for m6A peaks. The high m6A methylated genes (fat birds vs. lean birds) were primarily associated with fatty acid biosynthesis and fatty acid metabolism, while the low m6A methylated genes were mainly involved in processes associated with development. Furthermore, we found that the mRNA levels of many genes may be regulated by m6A modification. This is the first comprehensive characterization of m6A patterns in the chicken adipose transcriptome, and provides a basis for studying the role of m6A modification in fat deposition.
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Affiliation(s)
- Bohan Cheng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Li Leng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Ziwei Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Weijia Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yang Jing
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yudong Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Shouzhi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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50
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Wang YN, Jin HZ. Transcriptome-Wide m 6A Methylation in Skin Lesions From Patients With Psoriasis Vulgaris. Front Cell Dev Biol 2020; 8:591629. [PMID: 33251217 PMCID: PMC7674922 DOI: 10.3389/fcell.2020.591629] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/14/2020] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) methylation, as the most prevalent internal RNA modification, has been revealed to play critical roles in various biological functions. In this study, we performed m6A transcriptome-wide profiling in three kinds of skin tissue: involved psoriatic skin (PP), uninvolved psoriatic skin (PN), and healthy control skin samples (NN). The findings revealed that transcripts of PP contained the fewest m6A peaks and lowest m6A peak density. The greatest differences of m6A methylation were observed in the PP vs. NN and PP vs. PN comparisons. Intriguingly, in these comparisons, hypermethylated m6A was mainly enriched within the CDSs and 3′UTRs, while hypomethylated m6A was not only enriched within CDSs and 3′UTRs, but also within 5′UTRs. GO and KEGG pathway analyses indicated that hypermethylated transcripts in PP were particularly associated with response-associated terms, cytokine production, and olfactory transduction. Meanwhile, hypomethylated transcripts in PP were mainly associated with development-related processes and the Wnt signaling pathway. In addition, we discovered that 19.3–48.4% of the differentially expressed transcripts in psoriasis vulgaris were modified by m6A, and that transcripts with lower expression were more preferentially modified by m6A. Moreover, upregulation of gene expression was often accompanied by upregulation of m6A methylation, suggesting a regulatory role of m6A in psoriasis vulgaris gene expression.
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Affiliation(s)
- Ya-Nan Wang
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hong-Zhong Jin
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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